Starting phenix.real_space_refine on Thu Jul 24 07:57:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vag_31840/07_2025/7vag_31840.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vag_31840/07_2025/7vag_31840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vag_31840/07_2025/7vag_31840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vag_31840/07_2025/7vag_31840.map" model { file = "/net/cci-nas-00/data/ceres_data/7vag_31840/07_2025/7vag_31840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vag_31840/07_2025/7vag_31840.cif" } resolution = 3.32 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 3676 2.51 5 N 912 2.21 5 O 1066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5697 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2344 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1669 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 15, 'TRANS': 205} Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1684 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Time building chain proxies: 3.90, per 1000 atoms: 0.68 Number of scatterers: 5697 At special positions: 0 Unit cell: (84.66, 72.21, 140.685, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1066 8.00 N 912 7.00 C 3676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " 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: 1.40 Conformation dependent library (CDL) restraints added in 719.5 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 38.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.661A pdb=" N GLY A 19 " --> pdb=" O PRO A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 45 removed outlier: 4.106A pdb=" N THR A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.617A pdb=" N ILE A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.840A pdb=" N ILE A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.698A pdb=" N ASN A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 209 removed outlier: 3.510A pdb=" N VAL A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix removed outlier: 3.526A pdb=" N PHE A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.528A pdb=" N THR A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 284 through 310 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.793A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 66 removed outlier: 3.743A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY H 66 " --> pdb=" O LYS H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 66' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.866A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.952A pdb=" N LEU L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.514A pdb=" N LEU L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.606A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.028A pdb=" N CYS H 96 " --> pdb=" O TYR H 110 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N TYR H 110 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG H 98 " --> pdb=" O PHE H 108 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR H 100 " --> pdb=" O HIS H 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 130 through 132 removed outlier: 4.340A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER H 187 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR H 184 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA H 176 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER H 186 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 161 removed outlier: 3.644A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.527A pdb=" N TYR L 92 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 21 through 23 removed outlier: 3.673A pdb=" N CYS L 23 " --> pdb=" O PHE L 77 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE L 77 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 122 through 123 removed outlier: 3.574A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 158 through 159 283 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1734 1.35 - 1.46: 1443 1.46 - 1.58: 2593 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 5835 Sorted by residual: bond pdb=" CA MET A 133 " pdb=" CB MET A 133 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.84e-02 2.95e+03 1.08e+00 bond pdb=" CB GLN H 179 " pdb=" CG GLN H 179 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.00e+00 bond pdb=" CA GLN H 179 " pdb=" CB GLN H 179 " ideal model delta sigma weight residual 1.533 1.549 -0.016 1.69e-02 3.50e+03 8.61e-01 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.57e-01 bond pdb=" CB MET A 256 " pdb=" CG MET A 256 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.25e-01 ... (remaining 5830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 7752 1.88 - 3.76: 135 3.76 - 5.64: 31 5.64 - 7.52: 9 7.52 - 9.39: 2 Bond angle restraints: 7929 Sorted by residual: angle pdb=" CA GLN H 179 " pdb=" CB GLN H 179 " pdb=" CG GLN H 179 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.09e+00 angle pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " pdb=" CG LEU A 150 " ideal model delta sigma weight residual 116.30 125.69 -9.39 3.50e+00 8.16e-02 7.20e+00 angle pdb=" CB MET A 133 " pdb=" CG MET A 133 " pdb=" SD MET A 133 " ideal model delta sigma weight residual 112.70 120.74 -8.04 3.00e+00 1.11e-01 7.19e+00 angle pdb=" N MET A 133 " pdb=" CA MET A 133 " pdb=" CB MET A 133 " ideal model delta sigma weight residual 111.66 107.78 3.88 1.56e+00 4.11e-01 6.18e+00 angle pdb=" CB MET A 39 " pdb=" CG MET A 39 " pdb=" SD MET A 39 " ideal model delta sigma weight residual 112.70 119.71 -7.01 3.00e+00 1.11e-01 5.45e+00 ... (remaining 7924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3179 17.95 - 35.90: 258 35.90 - 53.85: 33 53.85 - 71.80: 7 71.80 - 89.75: 4 Dihedral angle restraints: 3481 sinusoidal: 1329 harmonic: 2152 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 165.03 -72.03 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CB GLU L 192 " pdb=" CG GLU L 192 " pdb=" CD GLU L 192 " pdb=" OE1 GLU L 192 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA GLY A 132 " pdb=" C GLY A 132 " pdb=" N MET A 133 " pdb=" CA MET A 133 " ideal model delta harmonic sigma weight residual 180.00 -164.19 -15.81 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 3478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 550 0.029 - 0.058: 230 0.058 - 0.088: 80 0.088 - 0.117: 52 0.117 - 0.146: 6 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA ILE H 104 " pdb=" N ILE H 104 " pdb=" C ILE H 104 " pdb=" CB ILE H 104 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CG LEU A 118 " pdb=" CB LEU A 118 " pdb=" CD1 LEU A 118 " pdb=" CD2 LEU A 118 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CB ILE A 214 " pdb=" CA ILE A 214 " pdb=" CG1 ILE A 214 " pdb=" CG2 ILE A 214 " both_signs ideal model delta sigma weight residual False 2.64 2.77 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 915 not shown) Planarity restraints: 980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR H 213 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.78e+00 pdb=" C THR H 213 " 0.023 2.00e-02 2.50e+03 pdb=" O THR H 213 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL H 214 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 174 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO H 175 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO H 175 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 175 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 280 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 281 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.015 5.00e-02 4.00e+02 ... (remaining 977 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 77 2.67 - 3.23: 5522 3.23 - 3.78: 8655 3.78 - 4.34: 11118 4.34 - 4.90: 18741 Nonbonded interactions: 44113 Sorted by model distance: nonbonded pdb=" OG SER H 198 " pdb=" OE1 GLN H 199 " model vdw 2.109 3.040 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 115 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" O SER A 126 " model vdw 2.293 3.040 nonbonded pdb=" OE2 GLU A 47 " pdb=" NZ LYS A 50 " model vdw 2.295 3.120 nonbonded pdb=" NH2 ARG L 60 " pdb=" O VAL L 64 " model vdw 2.317 3.120 ... (remaining 44108 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.690 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5838 Z= 0.111 Angle : 0.655 9.395 7935 Z= 0.311 Chirality : 0.041 0.146 918 Planarity : 0.004 0.031 980 Dihedral : 13.266 89.754 2096 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.15 % Allowed : 0.77 % Favored : 99.07 % 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: 0.41 (0.32), residues: 737 helix: 1.46 (0.33), residues: 250 sheet: 0.88 (0.41), residues: 168 loop : -1.04 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 56 HIS 0.002 0.000 HIS H 35 PHE 0.014 0.001 PHE A 292 TYR 0.010 0.001 TYR A 146 ARG 0.005 0.001 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.16855 ( 278) hydrogen bonds : angle 6.48913 ( 753) SS BOND : bond 0.00417 ( 3) SS BOND : angle 0.31508 ( 6) covalent geometry : bond 0.00239 ( 5835) covalent geometry : angle 0.65510 ( 7929) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7666 (ttm-80) REVERT: A 229 MET cc_start: 0.8523 (tpt) cc_final: 0.8039 (tpt) REVERT: A 308 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7435 (tp30) REVERT: H 91 SER cc_start: 0.8947 (m) cc_final: 0.8706 (p) REVERT: H 153 TYR cc_start: 0.6429 (p90) cc_final: 0.5833 (p90) REVERT: L 144 PHE cc_start: 0.8461 (p90) cc_final: 0.8190 (p90) REVERT: L 180 MET cc_start: 0.8413 (ttp) cc_final: 0.8086 (ttt) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.1477 time to fit residues: 42.0467 Evaluate side-chains 185 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 293 GLN H 39 GLN H 113 GLN H 179 GLN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118122 restraints weight = 9333.890| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.54 r_work: 0.3282 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 5838 Z= 0.283 Angle : 0.829 10.841 7935 Z= 0.414 Chirality : 0.050 0.187 918 Planarity : 0.005 0.045 980 Dihedral : 4.826 19.734 794 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.10 % Allowed : 16.25 % Favored : 80.65 % 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: 0.03 (0.31), residues: 737 helix: 1.13 (0.33), residues: 255 sheet: 0.60 (0.41), residues: 169 loop : -1.26 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 196 HIS 0.007 0.002 HIS H 207 PHE 0.028 0.003 PHE A 292 TYR 0.027 0.002 TYR A 146 ARG 0.007 0.001 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 278) hydrogen bonds : angle 4.86206 ( 753) SS BOND : bond 0.01283 ( 3) SS BOND : angle 1.04032 ( 6) covalent geometry : bond 0.00657 ( 5835) covalent geometry : angle 0.82863 ( 7929) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.8193 (t80) cc_final: 0.7977 (t80) REVERT: A 180 ARG cc_start: 0.8287 (mtt90) cc_final: 0.8001 (ttm170) REVERT: A 184 MET cc_start: 0.5239 (mmp) cc_final: 0.4860 (mmt) REVERT: A 229 MET cc_start: 0.9159 (tpt) cc_final: 0.8640 (tpt) REVERT: H 153 TYR cc_start: 0.7195 (p90) cc_final: 0.6199 (p90) REVERT: L 4 MET cc_start: 0.8957 (mmm) cc_final: 0.7686 (mmm) REVERT: L 61 GLU cc_start: 0.9368 (tp30) cc_final: 0.9143 (tp30) REVERT: L 87 GLU cc_start: 0.8624 (pm20) cc_final: 0.8343 (pm20) REVERT: L 88 ASP cc_start: 0.8956 (m-30) cc_final: 0.8638 (m-30) REVERT: L 144 PHE cc_start: 0.8478 (p90) cc_final: 0.8139 (p90) REVERT: L 147 LYS cc_start: 0.6249 (tttt) cc_final: 0.6002 (mttt) outliers start: 20 outliers final: 14 residues processed: 211 average time/residue: 0.1375 time to fit residues: 39.3927 Evaluate side-chains 203 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 69 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 293 GLN H 39 GLN H 179 GLN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.155929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120343 restraints weight = 9254.912| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.46 r_work: 0.3311 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5838 Z= 0.157 Angle : 0.716 11.913 7935 Z= 0.347 Chirality : 0.045 0.202 918 Planarity : 0.004 0.040 980 Dihedral : 4.610 18.771 794 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.41 % Allowed : 19.97 % Favored : 76.63 % 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: 0.28 (0.32), residues: 737 helix: 1.54 (0.34), residues: 254 sheet: 0.65 (0.41), residues: 173 loop : -1.26 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.004 0.001 HIS H 207 PHE 0.027 0.002 PHE A 292 TYR 0.016 0.001 TYR H 183 ARG 0.006 0.001 ARG L 113 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 278) hydrogen bonds : angle 4.57554 ( 753) SS BOND : bond 0.00531 ( 3) SS BOND : angle 0.43616 ( 6) covalent geometry : bond 0.00371 ( 5835) covalent geometry : angle 0.71577 ( 7929) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8986 (mp) REVERT: A 180 ARG cc_start: 0.8284 (mtt90) cc_final: 0.7524 (ttm110) REVERT: A 184 MET cc_start: 0.5216 (mmp) cc_final: 0.4878 (mmt) REVERT: A 229 MET cc_start: 0.9149 (tpt) cc_final: 0.8848 (tpt) REVERT: A 253 THR cc_start: 0.9211 (t) cc_final: 0.8972 (t) REVERT: H 61 ASN cc_start: 0.8988 (t0) cc_final: 0.8667 (t0) REVERT: H 153 TYR cc_start: 0.7451 (p90) cc_final: 0.6540 (p90) REVERT: L 2 ILE cc_start: 0.8928 (mm) cc_final: 0.8687 (mm) REVERT: L 4 MET cc_start: 0.8839 (mmm) cc_final: 0.7688 (mmm) REVERT: L 27 GLN cc_start: 0.8337 (pm20) cc_final: 0.7924 (pm20) REVERT: L 61 GLU cc_start: 0.9320 (tp30) cc_final: 0.9030 (tp30) REVERT: L 88 ASP cc_start: 0.8933 (m-30) cc_final: 0.8708 (m-30) REVERT: L 144 PHE cc_start: 0.8455 (p90) cc_final: 0.8076 (p90) REVERT: L 161 GLN cc_start: 0.6407 (mp10) cc_final: 0.5548 (pm20) outliers start: 22 outliers final: 14 residues processed: 210 average time/residue: 0.1388 time to fit residues: 39.7827 Evaluate side-chains 210 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 194 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 0.0040 chunk 15 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 209 ASN A 293 GLN H 39 GLN H 179 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.158052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122680 restraints weight = 9502.646| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.58 r_work: 0.3345 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5838 Z= 0.125 Angle : 0.694 10.497 7935 Z= 0.330 Chirality : 0.043 0.192 918 Planarity : 0.004 0.036 980 Dihedral : 4.411 18.709 794 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.41 % Allowed : 21.21 % Favored : 75.39 % 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: 0.39 (0.32), residues: 737 helix: 1.72 (0.34), residues: 253 sheet: 0.73 (0.42), residues: 166 loop : -1.25 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.003 0.001 HIS A 54 PHE 0.020 0.001 PHE A 292 TYR 0.016 0.001 TYR L 145 ARG 0.004 0.000 ARG L 113 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 278) hydrogen bonds : angle 4.38544 ( 753) SS BOND : bond 0.00342 ( 3) SS BOND : angle 0.28758 ( 6) covalent geometry : bond 0.00290 ( 5835) covalent geometry : angle 0.69409 ( 7929) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8871 (m) cc_final: 0.8550 (p) REVERT: A 184 MET cc_start: 0.5191 (mmp) cc_final: 0.4883 (mmt) REVERT: A 229 MET cc_start: 0.9085 (tpt) cc_final: 0.8707 (tpt) REVERT: A 253 THR cc_start: 0.9121 (t) cc_final: 0.8840 (t) REVERT: A 289 TYR cc_start: 0.8856 (t80) cc_final: 0.8568 (t80) REVERT: A 294 LEU cc_start: 0.8787 (tt) cc_final: 0.8401 (tt) REVERT: H 61 ASN cc_start: 0.8957 (t0) cc_final: 0.8595 (t0) REVERT: H 100 TYR cc_start: 0.8773 (t80) cc_final: 0.8494 (t80) REVERT: H 153 TYR cc_start: 0.7444 (p90) cc_final: 0.6536 (p90) REVERT: L 2 ILE cc_start: 0.8899 (mm) cc_final: 0.8606 (mm) REVERT: L 27 GLN cc_start: 0.8286 (pm20) cc_final: 0.7835 (pm20) REVERT: L 61 GLU cc_start: 0.9333 (tp30) cc_final: 0.9037 (tp30) REVERT: L 88 ASP cc_start: 0.8915 (m-30) cc_final: 0.8697 (m-30) REVERT: L 144 PHE cc_start: 0.8540 (p90) cc_final: 0.8162 (p90) outliers start: 22 outliers final: 15 residues processed: 210 average time/residue: 0.1422 time to fit residues: 40.8686 Evaluate side-chains 213 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 50 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 293 GLN H 39 GLN H 179 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.152701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117601 restraints weight = 9430.537| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.45 r_work: 0.3251 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5838 Z= 0.231 Angle : 0.770 9.515 7935 Z= 0.377 Chirality : 0.047 0.201 918 Planarity : 0.004 0.041 980 Dihedral : 4.815 20.725 794 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 5.42 % Allowed : 22.29 % Favored : 72.29 % 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: 0.04 (0.32), residues: 737 helix: 1.57 (0.34), residues: 248 sheet: 0.26 (0.41), residues: 175 loop : -1.39 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 168 HIS 0.004 0.001 HIS H 35 PHE 0.030 0.002 PHE A 292 TYR 0.017 0.002 TYR H 95 ARG 0.003 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 278) hydrogen bonds : angle 4.54895 ( 753) SS BOND : bond 0.00634 ( 3) SS BOND : angle 0.68977 ( 6) covalent geometry : bond 0.00545 ( 5835) covalent geometry : angle 0.77037 ( 7929) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.9173 (tpt) cc_final: 0.8740 (tpt) REVERT: A 253 THR cc_start: 0.9297 (t) cc_final: 0.9082 (t) REVERT: H 61 ASN cc_start: 0.8997 (t0) cc_final: 0.8578 (t0) REVERT: L 2 ILE cc_start: 0.8968 (mm) cc_final: 0.8734 (mm) REVERT: L 4 MET cc_start: 0.8951 (mmm) cc_final: 0.8529 (mmm) REVERT: L 42 TYR cc_start: 0.8996 (m-80) cc_final: 0.8728 (m-80) REVERT: L 61 GLU cc_start: 0.9287 (tp30) cc_final: 0.9034 (tp30) REVERT: L 88 ASP cc_start: 0.8925 (m-30) cc_final: 0.8708 (m-30) REVERT: L 144 PHE cc_start: 0.8434 (p90) cc_final: 0.8181 (p90) REVERT: L 161 GLN cc_start: 0.6536 (mp10) cc_final: 0.6306 (mp10) REVERT: L 180 MET cc_start: 0.8550 (ttt) cc_final: 0.8028 (ttt) outliers start: 35 outliers final: 26 residues processed: 214 average time/residue: 0.1415 time to fit residues: 40.8637 Evaluate side-chains 215 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 194 HIS Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN H 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118145 restraints weight = 9355.503| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.45 r_work: 0.3289 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5838 Z= 0.147 Angle : 0.743 9.831 7935 Z= 0.354 Chirality : 0.044 0.198 918 Planarity : 0.004 0.039 980 Dihedral : 4.690 20.510 794 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.33 % Allowed : 25.08 % Favored : 70.59 % 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: 0.06 (0.32), residues: 737 helix: 1.66 (0.34), residues: 247 sheet: 0.17 (0.41), residues: 174 loop : -1.39 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.026 0.001 PHE A 292 TYR 0.022 0.001 TYR L 145 ARG 0.006 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 278) hydrogen bonds : angle 4.47270 ( 753) SS BOND : bond 0.00414 ( 3) SS BOND : angle 0.40380 ( 6) covalent geometry : bond 0.00349 ( 5835) covalent geometry : angle 0.74278 ( 7929) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 127 THR cc_start: 0.8854 (m) cc_final: 0.8543 (p) REVERT: A 253 THR cc_start: 0.9202 (t) cc_final: 0.8937 (t) REVERT: A 294 LEU cc_start: 0.8746 (tt) cc_final: 0.8507 (tt) REVERT: H 61 ASN cc_start: 0.8933 (t0) cc_final: 0.8598 (t0) REVERT: H 100 TYR cc_start: 0.8772 (t80) cc_final: 0.8476 (t80) REVERT: H 179 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: L 2 ILE cc_start: 0.8943 (mm) cc_final: 0.8440 (mm) REVERT: L 27 GLN cc_start: 0.8479 (pm20) cc_final: 0.7623 (pm20) REVERT: L 61 GLU cc_start: 0.9324 (tp30) cc_final: 0.9095 (tp30) REVERT: L 88 ASP cc_start: 0.8930 (m-30) cc_final: 0.8728 (m-30) REVERT: L 144 PHE cc_start: 0.8298 (p90) cc_final: 0.8029 (p90) REVERT: L 161 GLN cc_start: 0.6445 (mp10) cc_final: 0.5694 (mp10) outliers start: 28 outliers final: 23 residues processed: 207 average time/residue: 0.1779 time to fit residues: 49.9227 Evaluate side-chains 219 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 194 HIS Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN H 39 GLN H 179 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.154983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.119021 restraints weight = 9435.162| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.52 r_work: 0.3303 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5838 Z= 0.141 Angle : 0.729 9.306 7935 Z= 0.349 Chirality : 0.044 0.206 918 Planarity : 0.004 0.039 980 Dihedral : 4.602 20.333 794 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.80 % Allowed : 25.23 % Favored : 69.97 % 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: 0.11 (0.32), residues: 737 helix: 1.77 (0.34), residues: 246 sheet: 0.13 (0.41), residues: 174 loop : -1.36 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 168 HIS 0.003 0.001 HIS A 54 PHE 0.023 0.001 PHE A 292 TYR 0.019 0.001 TYR L 145 ARG 0.010 0.001 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 278) hydrogen bonds : angle 4.42031 ( 753) SS BOND : bond 0.00382 ( 3) SS BOND : angle 0.37049 ( 6) covalent geometry : bond 0.00336 ( 5835) covalent geometry : angle 0.72896 ( 7929) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.9270 (tpp) cc_final: 0.8867 (tpp) REVERT: A 229 MET cc_start: 0.9220 (tpt) cc_final: 0.8691 (tpt) REVERT: A 253 THR cc_start: 0.9163 (t) cc_final: 0.8880 (t) REVERT: A 294 LEU cc_start: 0.8771 (tt) cc_final: 0.8542 (tt) REVERT: H 3 GLN cc_start: 0.9078 (pm20) cc_final: 0.8724 (pm20) REVERT: H 61 ASN cc_start: 0.8945 (t0) cc_final: 0.8575 (t0) REVERT: H 100 TYR cc_start: 0.8772 (t80) cc_final: 0.8481 (t80) REVERT: L 2 ILE cc_start: 0.8923 (mm) cc_final: 0.8695 (mm) REVERT: L 61 GLU cc_start: 0.9325 (tp30) cc_final: 0.9084 (tp30) REVERT: L 161 GLN cc_start: 0.6489 (mp10) cc_final: 0.5770 (mp10) REVERT: L 180 MET cc_start: 0.8479 (ttt) cc_final: 0.7963 (ttt) outliers start: 31 outliers final: 27 residues processed: 208 average time/residue: 0.1343 time to fit residues: 38.9841 Evaluate side-chains 221 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 194 HIS Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 209 ASN H 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119292 restraints weight = 9338.864| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.47 r_work: 0.3297 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5838 Z= 0.149 Angle : 0.747 10.534 7935 Z= 0.355 Chirality : 0.045 0.205 918 Planarity : 0.004 0.040 980 Dihedral : 4.596 20.606 794 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.49 % Allowed : 26.47 % Favored : 69.04 % 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: 0.04 (0.32), residues: 737 helix: 1.76 (0.34), residues: 246 sheet: 0.07 (0.41), residues: 174 loop : -1.42 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.031 0.002 PHE L 144 TYR 0.017 0.001 TYR L 145 ARG 0.007 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 278) hydrogen bonds : angle 4.43476 ( 753) SS BOND : bond 0.00409 ( 3) SS BOND : angle 0.42213 ( 6) covalent geometry : bond 0.00355 ( 5835) covalent geometry : angle 0.74719 ( 7929) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9256 (tpp) cc_final: 0.8950 (tpp) REVERT: A 127 THR cc_start: 0.8866 (m) cc_final: 0.8594 (p) REVERT: A 163 LEU cc_start: 0.9059 (tp) cc_final: 0.8731 (mp) REVERT: A 229 MET cc_start: 0.9208 (tpt) cc_final: 0.8721 (tpt) REVERT: A 253 THR cc_start: 0.9183 (t) cc_final: 0.8901 (t) REVERT: A 294 LEU cc_start: 0.8798 (tt) cc_final: 0.8571 (tt) REVERT: H 3 GLN cc_start: 0.9036 (pm20) cc_final: 0.8650 (pm20) REVERT: H 43 GLN cc_start: 0.8039 (mp10) cc_final: 0.7829 (mm-40) REVERT: H 61 ASN cc_start: 0.8883 (t0) cc_final: 0.8538 (t0) REVERT: H 100 TYR cc_start: 0.8776 (t80) cc_final: 0.8490 (t80) REVERT: H 179 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: L 2 ILE cc_start: 0.8924 (mm) cc_final: 0.8703 (mm) REVERT: L 61 GLU cc_start: 0.9326 (tp30) cc_final: 0.9089 (tp30) REVERT: L 161 GLN cc_start: 0.6648 (mp10) cc_final: 0.5944 (mp10) REVERT: L 180 MET cc_start: 0.8431 (ttt) cc_final: 0.7978 (ttt) outliers start: 29 outliers final: 28 residues processed: 203 average time/residue: 0.1318 time to fit residues: 37.3718 Evaluate side-chains 222 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 194 HIS Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN H 39 GLN H 179 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.150236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114828 restraints weight = 9426.766| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.39 r_work: 0.3249 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5838 Z= 0.210 Angle : 0.786 12.914 7935 Z= 0.380 Chirality : 0.047 0.205 918 Planarity : 0.004 0.045 980 Dihedral : 4.904 21.704 794 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.26 % Allowed : 25.85 % Favored : 68.89 % 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: -0.22 (0.32), residues: 737 helix: 1.50 (0.34), residues: 252 sheet: -0.13 (0.40), residues: 180 loop : -1.59 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.004 0.001 HIS H 35 PHE 0.032 0.002 PHE A 292 TYR 0.020 0.002 TYR A 146 ARG 0.009 0.001 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 278) hydrogen bonds : angle 4.59291 ( 753) SS BOND : bond 0.00594 ( 3) SS BOND : angle 0.66283 ( 6) covalent geometry : bond 0.00498 ( 5835) covalent geometry : angle 0.78634 ( 7929) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.9217 (tpt) cc_final: 0.8779 (tpt) REVERT: A 253 THR cc_start: 0.9254 (t) cc_final: 0.9014 (t) REVERT: A 256 MET cc_start: 0.7981 (ptm) cc_final: 0.7715 (ppp) REVERT: A 294 LEU cc_start: 0.8870 (tt) cc_final: 0.8662 (tt) REVERT: H 3 GLN cc_start: 0.9076 (pm20) cc_final: 0.8682 (pm20) REVERT: H 20 MET cc_start: 0.9059 (mtt) cc_final: 0.8577 (mtt) REVERT: H 61 ASN cc_start: 0.8934 (t0) cc_final: 0.8590 (t0) REVERT: H 100 TYR cc_start: 0.8806 (t80) cc_final: 0.8500 (t80) REVERT: H 151 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7592 (mmmm) REVERT: L 2 ILE cc_start: 0.8974 (mm) cc_final: 0.8774 (mm) REVERT: L 4 MET cc_start: 0.8887 (mmm) cc_final: 0.8509 (mmm) REVERT: L 42 TYR cc_start: 0.8977 (m-80) cc_final: 0.8740 (m-80) REVERT: L 61 GLU cc_start: 0.9346 (tp30) cc_final: 0.9115 (tp30) REVERT: L 161 GLN cc_start: 0.6865 (mp10) cc_final: 0.6051 (mp10) REVERT: L 180 MET cc_start: 0.8406 (ttt) cc_final: 0.7956 (ttt) outliers start: 34 outliers final: 31 residues processed: 211 average time/residue: 0.1447 time to fit residues: 41.1719 Evaluate side-chains 224 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 151 LYS Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 194 HIS Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 20 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117993 restraints weight = 9514.081| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.50 r_work: 0.3281 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5838 Z= 0.145 Angle : 0.770 11.095 7935 Z= 0.365 Chirality : 0.045 0.211 918 Planarity : 0.004 0.044 980 Dihedral : 4.760 20.601 794 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.49 % Allowed : 27.24 % Favored : 68.27 % 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: -0.19 (0.32), residues: 737 helix: 1.51 (0.34), residues: 252 sheet: -0.11 (0.40), residues: 180 loop : -1.56 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.022 0.001 PHE A 292 TYR 0.018 0.001 TYR A 146 ARG 0.012 0.001 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 278) hydrogen bonds : angle 4.56590 ( 753) SS BOND : bond 0.00371 ( 3) SS BOND : angle 0.50465 ( 6) covalent geometry : bond 0.00344 ( 5835) covalent geometry : angle 0.76984 ( 7929) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.5300 (mmp) cc_final: 0.4152 (ppp) REVERT: A 253 THR cc_start: 0.9183 (t) cc_final: 0.8919 (t) REVERT: A 294 LEU cc_start: 0.8776 (tt) cc_final: 0.8555 (tt) REVERT: H 3 GLN cc_start: 0.9057 (pm20) cc_final: 0.8664 (pm20) REVERT: H 20 MET cc_start: 0.9029 (mtt) cc_final: 0.8503 (mtt) REVERT: H 61 ASN cc_start: 0.8858 (t0) cc_final: 0.8508 (t0) REVERT: H 100 TYR cc_start: 0.8767 (t80) cc_final: 0.8458 (t80) REVERT: L 2 ILE cc_start: 0.8924 (mm) cc_final: 0.8720 (mm) REVERT: L 4 MET cc_start: 0.8795 (mmm) cc_final: 0.8422 (mmm) REVERT: L 42 TYR cc_start: 0.8936 (m-80) cc_final: 0.8723 (m-80) REVERT: L 61 GLU cc_start: 0.9343 (tp30) cc_final: 0.9058 (tp30) REVERT: L 145 TYR cc_start: 0.6123 (t80) cc_final: 0.5604 (t80) REVERT: L 161 GLN cc_start: 0.6779 (mp10) cc_final: 0.6093 (mp10) REVERT: L 180 MET cc_start: 0.8391 (ttt) cc_final: 0.8016 (ttt) outliers start: 29 outliers final: 26 residues processed: 209 average time/residue: 0.1323 time to fit residues: 37.8086 Evaluate side-chains 221 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 194 HIS Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 6 GLN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116659 restraints weight = 9561.808| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.52 r_work: 0.3265 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5838 Z= 0.180 Angle : 0.794 13.689 7935 Z= 0.377 Chirality : 0.046 0.209 918 Planarity : 0.004 0.045 980 Dihedral : 4.855 20.998 794 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.42 % Allowed : 26.93 % Favored : 67.65 % 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: -0.30 (0.32), residues: 737 helix: 1.38 (0.34), residues: 252 sheet: -0.27 (0.39), residues: 191 loop : -1.53 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.004 0.001 HIS H 35 PHE 0.027 0.002 PHE A 292 TYR 0.021 0.002 TYR A 146 ARG 0.012 0.001 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 278) hydrogen bonds : angle 4.63973 ( 753) SS BOND : bond 0.00479 ( 3) SS BOND : angle 0.60053 ( 6) covalent geometry : bond 0.00431 ( 5835) covalent geometry : angle 0.79408 ( 7929) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3287.33 seconds wall clock time: 58 minutes 5.34 seconds (3485.34 seconds total)