Starting phenix.real_space_refine on Thu Jul 2 01:36:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zr7_74594/07_2026/9zr7_74594.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zr7_74594/07_2026/9zr7_74594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zr7_74594/07_2026/9zr7_74594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zr7_74594/07_2026/9zr7_74594.map" model { file = "/net/cci-nas-00/data/ceres_data/9zr7_74594/07_2026/9zr7_74594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zr7_74594/07_2026/9zr7_74594.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1795 atoms to isotropic. 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 P 2 5.49 5 S 12 5.16 5 C 2385 2.51 5 N 635 2.21 5 O 770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3804 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1970 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 8, 'TRANS': 252} Chain breaks: 3 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "H" Number of atoms: 978 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 969 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Conformer: "B" Number of residues, atoms: 125, 969 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} bond proxies already assigned to first conformer: 988 Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.14, per 1000 atoms: 0.30 Number of scatterers: 3804 At special positions: 0 Unit cell: (61.05, 94.875, 82.5, 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 12 16.00 P 2 15.00 O 770 8.00 N 635 7.00 C 2385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 208.2 milliseconds 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 928 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 7 sheets defined 31.2% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 67 through 75 removed outlier: 3.837A pdb=" N TYR A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 92 through 105 removed outlier: 4.072A pdb=" N GLU A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 153 through 164 removed outlier: 4.499A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 removed outlier: 4.091A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 179 " --> pdb=" O TRP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 206 removed outlier: 3.700A pdb=" N ASP A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N MET A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.631A pdb=" N LYS A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 235 through 247 removed outlier: 3.734A pdb=" N ASP A 241 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 270 Processing helix chain 'H' and resid 107 through 112 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.885A pdb=" N LEU A 6 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE A 78 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL A 114 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A 80 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN A 116 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE A 82 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.749A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 14 through 15 removed outlier: 7.051A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR H 53 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.463A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.463A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 402 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: 0.52 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 916 1.33 - 1.45: 796 1.45 - 1.57: 2139 1.57 - 1.69: 5 1.69 - 1.81: 20 Bond restraints: 3876 Sorted by residual: bond pdb=" C4' GDP A 401 " pdb=" O4' GDP A 401 " ideal model delta sigma weight residual 1.426 1.620 -0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" C4' GDP A 401 " pdb=" C3' GDP A 401 " ideal model delta sigma weight residual 1.524 1.346 0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" N3 GDP A 401 " pdb=" C4 GDP A 401 " ideal model delta sigma weight residual 1.355 1.509 -0.154 2.00e-02 2.50e+03 5.91e+01 bond pdb=" N1 GDP A 401 " pdb=" C2 GDP A 401 " ideal model delta sigma weight residual 1.337 1.474 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" O4' GDP A 401 " pdb=" C1' GDP A 401 " ideal model delta sigma weight residual 1.426 1.310 0.116 2.00e-02 2.50e+03 3.34e+01 ... (remaining 3871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 5112 2.58 - 5.16: 127 5.16 - 7.75: 21 7.75 - 10.33: 5 10.33 - 12.91: 3 Bond angle restraints: 5268 Sorted by residual: angle pdb=" N GLY L 69 " pdb=" CA GLY L 69 " pdb=" C GLY L 69 " ideal model delta sigma weight residual 113.18 101.57 11.61 2.37e+00 1.78e-01 2.40e+01 angle pdb=" N TYR A 166 " pdb=" CA TYR A 166 " pdb=" C TYR A 166 " ideal model delta sigma weight residual 112.57 107.14 5.43 1.13e+00 7.83e-01 2.31e+01 angle pdb=" N GLN A 165 " pdb=" CA GLN A 165 " pdb=" C GLN A 165 " ideal model delta sigma weight residual 112.89 118.58 -5.69 1.24e+00 6.50e-01 2.10e+01 angle pdb=" N LEU L 93 " pdb=" CA LEU L 93 " pdb=" C LEU L 93 " ideal model delta sigma weight residual 111.33 116.80 -5.47 1.21e+00 6.83e-01 2.04e+01 angle pdb=" C TRP H 50 " pdb=" N VAL H 51 " pdb=" CA VAL H 51 " ideal model delta sigma weight residual 122.66 118.39 4.27 9.70e-01 1.06e+00 1.94e+01 ... (remaining 5263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 2224 35.63 - 71.25: 92 71.25 - 106.88: 7 106.88 - 142.51: 1 142.51 - 178.13: 1 Dihedral angle restraints: 2325 sinusoidal: 883 harmonic: 1442 Sorted by residual: dihedral pdb=" C5' GDP A 401 " pdb=" O5' GDP A 401 " pdb=" PA GDP A 401 " pdb=" O3A GDP A 401 " ideal model delta sinusoidal sigma weight residual 179.98 -1.89 -178.13 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2B GDP A 401 " pdb=" O3A GDP A 401 " pdb=" PB GDP A 401 " pdb=" PA GDP A 401 " ideal model delta sinusoidal sigma weight residual 180.00 62.40 117.60 1 2.00e+01 2.50e-03 3.51e+01 dihedral pdb=" CA TYR H 116 " pdb=" C TYR H 116 " pdb=" N TRP H 117 " pdb=" CA TRP H 117 " ideal model delta harmonic sigma weight residual 180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 2322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 546 0.109 - 0.218: 44 0.218 - 0.327: 3 0.327 - 0.436: 1 0.436 - 0.545: 1 Chirality restraints: 595 Sorted by residual: chirality pdb=" CA ARG A 164 " pdb=" N ARG A 164 " pdb=" C ARG A 164 " pdb=" CB ARG A 164 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.42e+00 chirality pdb=" CA TYR L 92 " pdb=" N TYR L 92 " pdb=" C TYR L 92 " pdb=" CB TYR L 92 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C3' GDP A 401 " pdb=" C4' GDP A 401 " pdb=" O3' GDP A 401 " pdb=" C2' GDP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.19 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 592 not shown) Planarity restraints: 675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " 0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO H 109 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 164 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C ARG A 164 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG A 164 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN A 165 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 80 " -0.043 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO L 81 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO L 81 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 81 " -0.036 5.00e-02 4.00e+02 ... (remaining 672 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 951 2.79 - 3.32: 3065 3.32 - 3.85: 6379 3.85 - 4.37: 7082 4.37 - 4.90: 12429 Nonbonded interactions: 29906 Sorted by model distance: nonbonded pdb=" NE ARG A 202 " pdb=" O LEU L 93 " model vdw 2.263 3.120 nonbonded pdb=" O ASP A 234 " pdb=" NE1 TRP H 105 " model vdw 2.289 3.120 nonbonded pdb=" CB ALA A 203 " pdb=" O SER L 29 " model vdw 2.309 3.460 nonbonded pdb=" O SER L 51 " pdb=" OG SER L 51 " model vdw 2.312 3.040 nonbonded pdb=" CE2 TYR L 94 " pdb=" OG SER L 96 " model vdw 2.315 3.340 ... (remaining 29901 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.930 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 0.009 0.194 3878 Z= 0.441 Angle : 1.028 12.911 5272 Z= 0.575 Chirality : 0.067 0.545 595 Planarity : 0.008 0.089 675 Dihedral : 19.098 178.135 1391 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 8.02 % Allowed : 22.56 % Favored : 69.42 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.97 (0.30), residues: 484 helix: -3.93 (0.22), residues: 143 sheet: -2.57 (0.39), residues: 149 loop : -3.13 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.029 0.002 TYR L 92 PHE 0.022 0.003 PHE A 156 TRP 0.015 0.002 TRP H 50 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00879 / 0.44 ( 3876) covalent geometry : angle 1.02791 / 0.58 ( 5268) SS BOND : bond 0.00562 / 0.29 ( 2) SS BOND : angle 1.23357 / 0.65 ( 4) hydrogen bonds : bond 0.21989 / 14.92 ( 144) hydrogen bonds : angle 9.79832 / 6.66 ( 402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.142 Fit side-chains REVERT: A 41 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6309 (mmt-90) REVERT: A 63 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7154 (pt0) REVERT: A 67 MET cc_start: 0.5661 (tpp) cc_final: 0.5048 (mpp) REVERT: A 156 PHE cc_start: 0.5829 (OUTLIER) cc_final: 0.5628 (t80) REVERT: A 248 ASN cc_start: 0.7683 (m-40) cc_final: 0.7409 (m110) REVERT: A 263 LYS cc_start: 0.7542 (pttm) cc_final: 0.7316 (pttm) REVERT: H 85 GLN cc_start: 0.6748 (mp10) cc_final: 0.6249 (mp10) REVERT: H 126 PHE cc_start: 0.6095 (t80) cc_final: 0.3796 (p90) REVERT: L 48 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6817 (mt) outliers start: 30 outliers final: 14 residues processed: 103 average time/residue: 0.0819 time to fit residues: 10.2114 Evaluate side-chains 79 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain H residue 99 CYS Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.185767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.137612 restraints weight = 14306.194| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 5.14 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3878 Z= 0.137 Angle : 0.597 6.212 5272 Z= 0.316 Chirality : 0.043 0.147 595 Planarity : 0.005 0.044 675 Dihedral : 12.231 166.721 577 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.76 % Allowed : 25.31 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.35), residues: 484 helix: -2.14 (0.35), residues: 146 sheet: -1.90 (0.45), residues: 135 loop : -2.62 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 266 TYR 0.016 0.002 TYR A 71 PHE 0.013 0.002 PHE H 35 TRP 0.021 0.002 TRP H 110 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 3876) covalent geometry : angle 0.59667 / 0.32 ( 5268) SS BOND : bond 0.00490 / 0.24 ( 2) SS BOND : angle 0.99300 / 0.55 ( 4) hydrogen bonds : bond 0.03415 / 2.28 ( 144) hydrogen bonds : angle 5.94746 / 3.90 ( 402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.5572 (tpp) cc_final: 0.4781 (mpp) REVERT: A 72 MET cc_start: 0.6178 (mtt) cc_final: 0.5932 (ttm) REVERT: A 156 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5244 (t80) REVERT: H 6 GLN cc_start: 0.8019 (tp-100) cc_final: 0.7700 (tp-100) REVERT: H 85 GLN cc_start: 0.7141 (mp10) cc_final: 0.6851 (mp10) REVERT: H 108 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6191 (mp0) REVERT: H 112 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7684 (mtmm) REVERT: H 126 PHE cc_start: 0.6146 (t80) cc_final: 0.3781 (p90) REVERT: L 108 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.4981 (mm) outliers start: 17 outliers final: 11 residues processed: 84 average time/residue: 0.0773 time to fit residues: 7.9531 Evaluate side-chains 78 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 33 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.177618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.128517 restraints weight = 11947.200| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 4.20 r_work: 0.3524 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3878 Z= 0.300 Angle : 0.734 8.341 5272 Z= 0.385 Chirality : 0.048 0.168 595 Planarity : 0.006 0.075 675 Dihedral : 11.515 141.373 556 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.34 % Favored : 90.46 % Rotamer: Outliers : 7.27 % Allowed : 23.56 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.38), residues: 484 helix: -1.51 (0.39), residues: 145 sheet: -1.90 (0.47), residues: 138 loop : -2.09 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 67 TYR 0.025 0.003 TYR L 92 PHE 0.026 0.003 PHE H 35 TRP 0.014 0.003 TRP H 50 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.30 ( 3876) covalent geometry : angle 0.73209 / 0.38 ( 5268) SS BOND : bond 0.00418 / 0.22 ( 2) SS BOND : angle 1.93449 / 1.11 ( 4) hydrogen bonds : bond 0.03846 / 2.52 ( 144) hydrogen bonds : angle 5.95274 / 3.89 ( 402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.153 Fit side-chains REVERT: A 67 MET cc_start: 0.5734 (tpp) cc_final: 0.4663 (mpp) REVERT: A 70 GLN cc_start: 0.5618 (OUTLIER) cc_final: 0.4874 (tp40) REVERT: A 156 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.5951 (t80) REVERT: A 244 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7412 (tt) REVERT: A 248 ASN cc_start: 0.8093 (m-40) cc_final: 0.7602 (m110) REVERT: H 6 GLN cc_start: 0.8117 (tp-100) cc_final: 0.7855 (tp-100) REVERT: H 22 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7591 (mmm160) REVERT: H 85 GLN cc_start: 0.7610 (mp10) cc_final: 0.7204 (mp10) REVERT: H 126 PHE cc_start: 0.6356 (t80) cc_final: 0.4041 (p90) REVERT: L 5 MET cc_start: 0.7977 (mtp) cc_final: 0.7700 (mtp) REVERT: L 108 ILE cc_start: 0.6355 (OUTLIER) cc_final: 0.5612 (mm) outliers start: 27 outliers final: 17 residues processed: 82 average time/residue: 0.0825 time to fit residues: 8.1294 Evaluate side-chains 77 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.179899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.133363 restraints weight = 13745.279| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 5.10 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3878 Z= 0.149 Angle : 0.589 6.088 5272 Z= 0.306 Chirality : 0.044 0.143 595 Planarity : 0.005 0.067 675 Dihedral : 10.503 132.350 556 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.76 % Allowed : 27.07 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.39), residues: 484 helix: -0.88 (0.42), residues: 145 sheet: -1.61 (0.47), residues: 138 loop : -2.01 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 101 TYR 0.017 0.002 TYR A 71 PHE 0.019 0.002 PHE H 35 TRP 0.015 0.002 TRP H 110 HIS 0.001 0.000 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 3876) covalent geometry : angle 0.58786 / 0.31 ( 5268) SS BOND : bond 0.00628 / 0.31 ( 2) SS BOND : angle 1.37546 / 0.75 ( 4) hydrogen bonds : bond 0.02933 / 1.95 ( 144) hydrogen bonds : angle 5.43356 / 3.58 ( 402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.5981 (mmm160) REVERT: A 67 MET cc_start: 0.5755 (tpp) cc_final: 0.4667 (mpp) REVERT: A 70 GLN cc_start: 0.5518 (OUTLIER) cc_final: 0.4673 (tp40) REVERT: A 156 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.5013 (t80) REVERT: H 22 ARG cc_start: 0.7581 (mmm160) cc_final: 0.7166 (mmm160) REVERT: H 85 GLN cc_start: 0.7352 (mp10) cc_final: 0.6671 (mp10) REVERT: H 126 PHE cc_start: 0.6382 (t80) cc_final: 0.4204 (p90) REVERT: L 25 ARG cc_start: 0.7207 (ttp-110) cc_final: 0.6765 (ttp-110) REVERT: L 108 ILE cc_start: 0.5637 (OUTLIER) cc_final: 0.5068 (mm) outliers start: 21 outliers final: 12 residues processed: 79 average time/residue: 0.0864 time to fit residues: 8.1820 Evaluate side-chains 78 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.177097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.131415 restraints weight = 16597.600| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 6.43 r_work: 0.3445 rms_B_bonded: 6.27 restraints_weight: 2.0000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3878 Z= 0.196 Angle : 0.642 7.419 5272 Z= 0.328 Chirality : 0.045 0.149 595 Planarity : 0.005 0.062 675 Dihedral : 10.290 126.876 554 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 7.02 % Allowed : 27.07 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.39), residues: 484 helix: -0.84 (0.42), residues: 147 sheet: -1.60 (0.46), residues: 138 loop : -2.03 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 67 TYR 0.019 0.002 TYR L 92 PHE 0.015 0.002 PHE A 82 TRP 0.015 0.002 TRP H 50 HIS 0.000 0.000 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 ( 3876) covalent geometry : angle 0.64023 / 0.33 ( 5268) SS BOND : bond 0.00554 / 0.28 ( 2) SS BOND : angle 1.95788 / 1.14 ( 4) hydrogen bonds : bond 0.03066 / 2.04 ( 144) hydrogen bonds : angle 5.48605 / 3.62 ( 402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.5860 (tpp) cc_final: 0.4783 (mpp) REVERT: A 70 GLN cc_start: 0.5663 (OUTLIER) cc_final: 0.4920 (tp40) REVERT: A 156 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.5439 (t80) REVERT: H 85 GLN cc_start: 0.7681 (mp10) cc_final: 0.7086 (mp10) REVERT: H 126 PHE cc_start: 0.6431 (t80) cc_final: 0.4089 (p90) REVERT: L 25 ARG cc_start: 0.7586 (ttp-110) cc_final: 0.6940 (ttp-110) REVERT: L 108 ILE cc_start: 0.6346 (OUTLIER) cc_final: 0.5631 (mm) outliers start: 26 outliers final: 18 residues processed: 85 average time/residue: 0.0893 time to fit residues: 9.0628 Evaluate side-chains 86 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 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 = 0.178577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.131228 restraints weight = 12639.023| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 4.98 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3878 Z= 0.126 Angle : 0.578 6.116 5272 Z= 0.292 Chirality : 0.043 0.144 595 Planarity : 0.004 0.041 675 Dihedral : 9.085 94.497 554 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.01 % Allowed : 31.33 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.39), residues: 484 helix: -0.48 (0.43), residues: 147 sheet: -1.29 (0.47), residues: 136 loop : -1.99 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.017 0.001 TYR A 71 PHE 0.012 0.002 PHE A 82 TRP 0.014 0.002 TRP H 50 HIS 0.001 0.000 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 3876) covalent geometry : angle 0.57626 / 0.29 ( 5268) SS BOND : bond 0.00520 / 0.26 ( 2) SS BOND : angle 1.60631 / 0.93 ( 4) hydrogen bonds : bond 0.02677 / 1.80 ( 144) hydrogen bonds : angle 5.13366 / 3.36 ( 402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.147 Fit side-chains REVERT: A 67 MET cc_start: 0.6015 (tpp) cc_final: 0.4903 (mpp) REVERT: A 70 GLN cc_start: 0.5580 (OUTLIER) cc_final: 0.4688 (tp40) REVERT: A 80 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7992 (mt) REVERT: A 156 PHE cc_start: 0.6199 (OUTLIER) cc_final: 0.4982 (t80) REVERT: A 266 ARG cc_start: 0.7710 (tmm-80) cc_final: 0.7486 (tmm-80) REVERT: H 85 GLN cc_start: 0.7461 (mp10) cc_final: 0.6872 (mp10) REVERT: H 126 PHE cc_start: 0.6167 (t80) cc_final: 0.4258 (p90) REVERT: L 25 ARG cc_start: 0.7159 (ttp-110) cc_final: 0.6702 (ttp-110) outliers start: 14 outliers final: 9 residues processed: 82 average time/residue: 0.0825 time to fit residues: 8.2133 Evaluate side-chains 77 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 0.6980 chunk 27 optimal weight: 0.0050 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.180242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.132394 restraints weight = 10549.267| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 4.16 r_work: 0.3566 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3878 Z= 0.125 Angle : 0.597 6.419 5272 Z= 0.301 Chirality : 0.044 0.143 595 Planarity : 0.004 0.040 675 Dihedral : 8.195 101.370 551 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 6.02 % Allowed : 29.57 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.39), residues: 484 helix: -0.44 (0.42), residues: 154 sheet: -1.15 (0.47), residues: 136 loop : -1.97 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 149 TYR 0.017 0.001 TYR A 71 PHE 0.018 0.002 PHE A 82 TRP 0.013 0.002 TRP H 110 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 3876) covalent geometry : angle 0.59592 / 0.30 ( 5268) SS BOND : bond 0.00508 / 0.25 ( 2) SS BOND : angle 1.47004 / 0.85 ( 4) hydrogen bonds : bond 0.02658 / 1.79 ( 144) hydrogen bonds : angle 5.00355 / 3.28 ( 402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.182 Fit side-chains REVERT: A 41 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6214 (mmm160) REVERT: A 67 MET cc_start: 0.5993 (tpp) cc_final: 0.4987 (mpp) REVERT: A 70 GLN cc_start: 0.5748 (OUTLIER) cc_final: 0.5033 (tp40) REVERT: A 80 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8165 (mt) REVERT: A 156 PHE cc_start: 0.6384 (OUTLIER) cc_final: 0.5155 (t80) REVERT: A 165 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7253 (mt0) REVERT: A 263 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7304 (pttm) REVERT: H 85 GLN cc_start: 0.7703 (mp10) cc_final: 0.7141 (mp10) REVERT: H 104 TYR cc_start: 0.7958 (m-10) cc_final: 0.7745 (m-10) REVERT: H 126 PHE cc_start: 0.6169 (t80) cc_final: 0.4263 (p90) REVERT: L 25 ARG cc_start: 0.7445 (ttp-110) cc_final: 0.6853 (tpt170) REVERT: L 108 ILE cc_start: 0.5845 (OUTLIER) cc_final: 0.5233 (mm) outliers start: 22 outliers final: 11 residues processed: 88 average time/residue: 0.0680 time to fit residues: 7.3159 Evaluate side-chains 82 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN H 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.179056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.133418 restraints weight = 9164.384| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.68 r_work: 0.3601 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3878 Z= 0.136 Angle : 0.624 7.998 5272 Z= 0.311 Chirality : 0.044 0.142 595 Planarity : 0.004 0.040 675 Dihedral : 7.800 91.862 551 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.26 % Allowed : 30.33 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.39), residues: 484 helix: -0.22 (0.43), residues: 154 sheet: -1.06 (0.47), residues: 136 loop : -1.88 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 149 TYR 0.017 0.001 TYR A 71 PHE 0.017 0.002 PHE A 82 TRP 0.013 0.002 TRP H 50 HIS 0.001 0.000 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 3876) covalent geometry : angle 0.62263 / 0.31 ( 5268) SS BOND : bond 0.00510 / 0.25 ( 2) SS BOND : angle 1.36639 / 0.77 ( 4) hydrogen bonds : bond 0.02748 / 1.92 ( 144) hydrogen bonds : angle 5.11133 / 3.33 ( 402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6237 (mmm160) REVERT: A 67 MET cc_start: 0.5990 (tpp) cc_final: 0.5048 (mpp) REVERT: A 70 GLN cc_start: 0.5672 (OUTLIER) cc_final: 0.5006 (tp40) REVERT: A 80 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8154 (mt) REVERT: A 156 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.5122 (t80) REVERT: A 165 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7231 (mt0) REVERT: H 85 GLN cc_start: 0.7692 (mp10) cc_final: 0.7156 (mp10) REVERT: H 126 PHE cc_start: 0.5933 (t80) cc_final: 0.3887 (p90) REVERT: L 25 ARG cc_start: 0.7378 (ttp-110) cc_final: 0.6823 (ttp-110) REVERT: L 108 ILE cc_start: 0.5933 (OUTLIER) cc_final: 0.5313 (mm) outliers start: 19 outliers final: 12 residues processed: 79 average time/residue: 0.0807 time to fit residues: 7.7014 Evaluate side-chains 79 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.0070 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.179740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.132670 restraints weight = 11190.299| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 4.05 r_work: 0.3593 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3878 Z= 0.149 Angle : 0.640 7.589 5272 Z= 0.320 Chirality : 0.045 0.141 595 Planarity : 0.004 0.041 675 Dihedral : 7.569 82.521 551 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 5.26 % Allowed : 31.08 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.40), residues: 484 helix: -0.07 (0.43), residues: 151 sheet: -1.16 (0.47), residues: 138 loop : -1.64 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 149 TYR 0.017 0.001 TYR A 71 PHE 0.017 0.002 PHE A 82 TRP 0.013 0.002 TRP H 50 HIS 0.001 0.000 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 3876) covalent geometry : angle 0.63876 / 0.32 ( 5268) SS BOND : bond 0.00514 / 0.26 ( 2) SS BOND : angle 1.42438 / 0.81 ( 4) hydrogen bonds : bond 0.02701 / 1.85 ( 144) hydrogen bonds : angle 4.97984 / 3.27 ( 402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6255 (mmm160) REVERT: A 67 MET cc_start: 0.6105 (tpp) cc_final: 0.5223 (mpp) REVERT: A 70 GLN cc_start: 0.5639 (OUTLIER) cc_final: 0.4704 (tp40) REVERT: A 156 PHE cc_start: 0.6384 (OUTLIER) cc_final: 0.5109 (t80) REVERT: A 263 LYS cc_start: 0.7908 (tmtt) cc_final: 0.7572 (pttm) REVERT: H 6 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7822 (tp-100) REVERT: H 85 GLN cc_start: 0.7658 (mp10) cc_final: 0.7046 (mp10) REVERT: H 126 PHE cc_start: 0.5770 (t80) cc_final: 0.3715 (p90) REVERT: L 25 ARG cc_start: 0.7371 (ttp-110) cc_final: 0.6814 (ttp-110) REVERT: L 108 ILE cc_start: 0.5917 (OUTLIER) cc_final: 0.5292 (mm) outliers start: 19 outliers final: 13 residues processed: 81 average time/residue: 0.0873 time to fit residues: 8.4707 Evaluate side-chains 81 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.179059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131737 restraints weight = 11910.269| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 4.49 r_work: 0.3561 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3878 Z= 0.163 Angle : 0.651 7.730 5272 Z= 0.327 Chirality : 0.045 0.147 595 Planarity : 0.004 0.044 675 Dihedral : 7.257 75.343 549 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.01 % Allowed : 31.83 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.40), residues: 484 helix: -0.07 (0.43), residues: 151 sheet: -1.18 (0.47), residues: 138 loop : -1.62 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 167 TYR 0.017 0.002 TYR A 71 PHE 0.017 0.002 PHE A 82 TRP 0.013 0.002 TRP H 50 HIS 0.001 0.000 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 3876) covalent geometry : angle 0.65012 / 0.33 ( 5268) SS BOND : bond 0.00529 / 0.26 ( 2) SS BOND : angle 1.50305 / 0.84 ( 4) hydrogen bonds : bond 0.02741 / 1.87 ( 144) hydrogen bonds : angle 4.95952 / 3.27 ( 402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.145 Fit side-chains REVERT: A 41 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6264 (mmm160) REVERT: A 67 MET cc_start: 0.6290 (tpp) cc_final: 0.5392 (mpp) REVERT: A 70 GLN cc_start: 0.5638 (OUTLIER) cc_final: 0.4730 (tp40) REVERT: A 156 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5120 (t80) REVERT: H 6 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7854 (tp-100) REVERT: H 22 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7513 (mmm160) REVERT: H 85 GLN cc_start: 0.7639 (mp10) cc_final: 0.6978 (mp10) REVERT: H 126 PHE cc_start: 0.5815 (t80) cc_final: 0.3582 (p90) REVERT: L 25 ARG cc_start: 0.7377 (ttp-110) cc_final: 0.6823 (ttp-110) REVERT: L 108 ILE cc_start: 0.6021 (OUTLIER) cc_final: 0.5360 (mm) outliers start: 18 outliers final: 13 residues processed: 78 average time/residue: 0.0920 time to fit residues: 8.5596 Evaluate side-chains 80 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.0060 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.183185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.135682 restraints weight = 12869.380| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 5.07 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3878 Z= 0.114 Angle : 0.608 7.349 5272 Z= 0.303 Chirality : 0.044 0.145 595 Planarity : 0.004 0.039 675 Dihedral : 6.653 59.420 549 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.76 % Allowed : 31.83 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.40), residues: 484 helix: 0.06 (0.43), residues: 155 sheet: -0.97 (0.46), residues: 143 loop : -1.54 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 167 TYR 0.017 0.001 TYR A 71 PHE 0.016 0.002 PHE A 82 TRP 0.014 0.001 TRP H 50 HIS 0.001 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 3876) covalent geometry : angle 0.60788 / 0.30 ( 5268) SS BOND : bond 0.00474 / 0.24 ( 2) SS BOND : angle 1.12080 / 0.64 ( 4) hydrogen bonds : bond 0.02502 / 1.73 ( 144) hydrogen bonds : angle 4.71142 / 3.11 ( 402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1283.75 seconds wall clock time: 22 minutes 40.62 seconds (1360.62 seconds total)