Starting phenix.real_space_refine on Tue Mar 3 13:49:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fci_31526/03_2026/7fci_31526.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fci_31526/03_2026/7fci_31526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fci_31526/03_2026/7fci_31526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fci_31526/03_2026/7fci_31526.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fci_31526/03_2026/7fci_31526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fci_31526/03_2026/7fci_31526.map" } resolution = 3.3 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= 0.003 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 47 5.16 5 C 3622 2.51 5 N 899 2.21 5 O 1045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5613 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2280 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1640 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Chain: "H" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1693 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 208} Time building chain proxies: 1.30, per 1000 atoms: 0.23 Number of scatterers: 5613 At special positions: 0 Unit cell: (57.201, 66.32, 135.127, 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 47 16.00 O 1045 8.00 N 899 7.00 C 3622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 337.1 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 41.4% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 20 through 43 removed outlier: 3.900A pdb=" N ASP A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.544A pdb=" N LYS A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.569A pdb=" N ILE A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 155 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 180 through 216 removed outlier: 3.824A pdb=" N MET A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG A 185 " --> pdb=" O PRO A 181 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.689A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 310 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.566A pdb=" N ASP L 81 " --> pdb=" O GLU L 78 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 82' Processing helix chain 'L' and resid 120 through 127 Processing helix chain 'L' and resid 182 through 188 removed outlier: 3.775A pdb=" N HIS L 188 " --> pdb=" O GLU L 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.057A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.529A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'H' and resid 195 through 200 Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.778A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.620A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 115 through 117 removed outlier: 3.852A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA7, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.597A pdb=" N GLU H 10 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.597A pdb=" N GLU H 10 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.703A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N CYS H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER H 188 " --> pdb=" O CYS H 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AB2, first strand: chain 'H' and resid 178 through 180 331 hydrogen bonds defined for protein. 915 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: 0.71 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1549 1.34 - 1.45: 1038 1.45 - 1.57: 3090 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 5749 Sorted by residual: bond pdb=" CB PRO A 220 " pdb=" CG PRO A 220 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.73e+00 bond pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CG PRO L 94 " pdb=" CD PRO L 94 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.09e+00 bond pdb=" CA VAL H 159 " pdb=" CB VAL H 159 " ideal model delta sigma weight residual 1.551 1.540 0.011 1.08e-02 8.57e+03 9.47e-01 bond pdb=" CA VAL H 106 " pdb=" CB VAL H 106 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.47e-02 4.63e+03 9.15e-01 ... (remaining 5744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 7696 2.01 - 4.01: 102 4.01 - 6.02: 15 6.02 - 8.02: 3 8.02 - 10.03: 1 Bond angle restraints: 7817 Sorted by residual: angle pdb=" CA GLU A 257 " pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA LEU A 165 " pdb=" CB LEU A 165 " pdb=" CG LEU A 165 " ideal model delta sigma weight residual 116.30 126.33 -10.03 3.50e+00 8.16e-02 8.21e+00 angle pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " pdb=" CD GLU A 257 " ideal model delta sigma weight residual 112.60 116.99 -4.39 1.70e+00 3.46e-01 6.68e+00 angle pdb=" CA TYR L 31 " pdb=" CB TYR L 31 " pdb=" CG TYR L 31 " ideal model delta sigma weight residual 113.90 118.30 -4.40 1.80e+00 3.09e-01 5.97e+00 angle pdb=" CA GLY H 115 " pdb=" C GLY H 115 " pdb=" O GLY H 115 " ideal model delta sigma weight residual 122.22 120.63 1.59 6.50e-01 2.37e+00 5.95e+00 ... (remaining 7812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 2913 16.35 - 32.69: 367 32.69 - 49.04: 124 49.04 - 65.38: 28 65.38 - 81.73: 4 Dihedral angle restraints: 3436 sinusoidal: 1310 harmonic: 2126 Sorted by residual: dihedral pdb=" CB CYS H 149 " pdb=" SG CYS H 149 " pdb=" SG CYS H 204 " pdb=" CB CYS H 204 " ideal model delta sinusoidal sigma weight residual 93.00 160.94 -67.94 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" CA ASN L 30 " pdb=" C ASN L 30 " pdb=" N TYR L 31 " pdb=" CA TYR L 31 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+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 -162.30 -17.70 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 533 0.027 - 0.054: 241 0.054 - 0.080: 70 0.080 - 0.107: 44 0.107 - 0.134: 20 Chirality restraints: 908 Sorted by residual: chirality pdb=" CA VAL H 206 " pdb=" N VAL H 206 " pdb=" C VAL H 206 " pdb=" CB VAL H 206 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL H 161 " pdb=" N VAL H 161 " pdb=" C VAL H 161 " pdb=" CB VAL H 161 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA PRO A 220 " pdb=" N PRO A 220 " pdb=" C PRO A 220 " pdb=" CB PRO A 220 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 905 not shown) Planarity restraints: 965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS H 208 " 0.063 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO H 209 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO H 209 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 209 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " -0.046 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO A 220 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 180 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO A 181 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.035 5.00e-02 4.00e+02 ... (remaining 962 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1142 2.78 - 3.31: 4982 3.31 - 3.84: 9209 3.84 - 4.37: 10533 4.37 - 4.90: 18948 Nonbonded interactions: 44814 Sorted by model distance: nonbonded pdb=" OG SER L 62 " pdb=" OG1 THR L 73 " model vdw 2.250 3.040 nonbonded pdb=" OE1 GLN A 68 " pdb=" OG SER A 126 " model vdw 2.260 3.040 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.266 3.040 nonbonded pdb=" OG SER L 120 " pdb=" O PRO H 132 " model vdw 2.271 3.040 nonbonded pdb=" NH1 ARG L 107 " pdb=" O ASP L 169 " model vdw 2.271 3.120 ... (remaining 44809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.730 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 0.003 0.066 5753 Z= 0.129 Angle : 0.595 10.026 7825 Z= 0.317 Chirality : 0.040 0.134 908 Planarity : 0.006 0.096 965 Dihedral : 16.431 81.730 2062 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.55 % Allowed : 27.79 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.59 (0.32), residues: 728 helix: 1.93 (0.34), residues: 258 sheet: 0.27 (0.38), residues: 198 loop : -1.02 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.012 0.001 TYR H 184 PHE 0.018 0.001 PHE H 155 TRP 0.017 0.001 TRP L 162 HIS 0.002 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5749) covalent geometry : angle 0.59559 ( 7817) SS BOND : bond 0.00244 ( 4) SS BOND : angle 0.42806 ( 8) hydrogen bonds : bond 0.13444 ( 319) hydrogen bonds : angle 6.28372 ( 915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.200 Fit side-chains REVERT: L 4 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7425 (mtp) REVERT: H 107 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6248 (p90) outliers start: 29 outliers final: 25 residues processed: 98 average time/residue: 0.0530 time to fit residues: 7.5205 Evaluate side-chains 99 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 117 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 0.0970 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.182940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126841 restraints weight = 6189.344| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.95 r_work: 0.2961 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5753 Z= 0.138 Angle : 0.547 8.067 7825 Z= 0.281 Chirality : 0.041 0.146 908 Planarity : 0.006 0.067 965 Dihedral : 8.297 69.437 822 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.71 % Allowed : 26.53 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.80 (0.33), residues: 728 helix: 2.00 (0.33), residues: 266 sheet: 0.26 (0.36), residues: 221 loop : -0.83 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.013 0.001 TYR H 154 PHE 0.011 0.001 PHE H 107 TRP 0.013 0.001 TRP L 90 HIS 0.003 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5749) covalent geometry : angle 0.54754 ( 7817) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.47551 ( 8) hydrogen bonds : bond 0.03824 ( 319) hydrogen bonds : angle 4.65030 ( 915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.182 Fit side-chains REVERT: A 257 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8267 (tm-30) REVERT: L 4 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8164 (mtp) REVERT: L 107 ARG cc_start: 0.8041 (ptm160) cc_final: 0.7761 (ptm160) REVERT: L 174 MET cc_start: 0.8185 (tpt) cc_final: 0.7826 (tpt) outliers start: 30 outliers final: 18 residues processed: 106 average time/residue: 0.0584 time to fit residues: 8.6175 Evaluate side-chains 95 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.0370 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 9 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.181359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140952 restraints weight = 6085.069| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.90 r_work: 0.2923 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5753 Z= 0.146 Angle : 0.541 6.830 7825 Z= 0.277 Chirality : 0.041 0.147 908 Planarity : 0.005 0.059 965 Dihedral : 6.994 69.508 796 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.24 % Allowed : 26.84 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.83 (0.33), residues: 728 helix: 2.03 (0.33), residues: 266 sheet: 0.27 (0.36), residues: 221 loop : -0.82 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.013 0.001 TYR H 154 PHE 0.011 0.001 PHE H 107 TRP 0.013 0.001 TRP L 90 HIS 0.002 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5749) covalent geometry : angle 0.54115 ( 7817) SS BOND : bond 0.00317 ( 4) SS BOND : angle 0.46076 ( 8) hydrogen bonds : bond 0.03845 ( 319) hydrogen bonds : angle 4.44950 ( 915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.202 Fit side-chains REVERT: A 184 MET cc_start: 0.2321 (tmt) cc_final: 0.1797 (ttt) REVERT: A 257 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8224 (tm-30) outliers start: 27 outliers final: 21 residues processed: 96 average time/residue: 0.0631 time to fit residues: 8.4654 Evaluate side-chains 93 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 0.0020 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.181055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.140524 restraints weight = 6081.720| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.90 r_work: 0.2894 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5753 Z= 0.142 Angle : 0.537 7.286 7825 Z= 0.274 Chirality : 0.041 0.148 908 Planarity : 0.005 0.054 965 Dihedral : 6.230 69.597 789 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.40 % Allowed : 26.37 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.83 (0.33), residues: 728 helix: 2.08 (0.32), residues: 266 sheet: 0.23 (0.36), residues: 221 loop : -0.82 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.012 0.001 TYR H 154 PHE 0.011 0.001 PHE H 107 TRP 0.013 0.001 TRP L 162 HIS 0.002 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5749) covalent geometry : angle 0.53664 ( 7817) SS BOND : bond 0.00327 ( 4) SS BOND : angle 0.46898 ( 8) hydrogen bonds : bond 0.03721 ( 319) hydrogen bonds : angle 4.35170 ( 915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.173 Fit side-chains REVERT: A 184 MET cc_start: 0.2416 (tmt) cc_final: 0.1948 (ttt) REVERT: A 196 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7728 (tm) REVERT: A 257 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8181 (tm-30) REVERT: L 107 ARG cc_start: 0.8080 (ptm160) cc_final: 0.7672 (ptm160) REVERT: L 174 MET cc_start: 0.8176 (tpt) cc_final: 0.7845 (tpt) REVERT: H 5 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7421 (tt0) outliers start: 28 outliers final: 22 residues processed: 100 average time/residue: 0.0529 time to fit residues: 7.5202 Evaluate side-chains 97 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 64 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.182201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.141198 restraints weight = 6178.264| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.83 r_work: 0.2936 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5753 Z= 0.125 Angle : 0.526 8.070 7825 Z= 0.266 Chirality : 0.040 0.147 908 Planarity : 0.005 0.050 965 Dihedral : 6.042 69.719 788 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.55 % Allowed : 26.69 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.89 (0.33), residues: 728 helix: 2.16 (0.32), residues: 266 sheet: 0.24 (0.36), residues: 221 loop : -0.82 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.012 0.001 TYR H 154 PHE 0.010 0.001 PHE H 107 TRP 0.012 0.001 TRP L 162 HIS 0.002 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5749) covalent geometry : angle 0.52639 ( 7817) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.39398 ( 8) hydrogen bonds : bond 0.03538 ( 319) hydrogen bonds : angle 4.26280 ( 915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.202 Fit side-chains REVERT: A 184 MET cc_start: 0.2511 (tmt) cc_final: 0.1914 (ttt) REVERT: A 196 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7672 (tm) REVERT: A 257 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8157 (tm-30) REVERT: H 5 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7474 (tt0) outliers start: 29 outliers final: 21 residues processed: 102 average time/residue: 0.0534 time to fit residues: 7.8345 Evaluate side-chains 96 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.181832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141227 restraints weight = 6123.605| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.96 r_work: 0.2947 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5753 Z= 0.135 Angle : 0.538 9.133 7825 Z= 0.271 Chirality : 0.041 0.148 908 Planarity : 0.005 0.048 965 Dihedral : 5.967 69.789 787 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.24 % Allowed : 27.00 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.87 (0.33), residues: 728 helix: 2.15 (0.32), residues: 266 sheet: 0.22 (0.36), residues: 221 loop : -0.83 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.012 0.001 TYR H 154 PHE 0.014 0.001 PHE A 37 TRP 0.014 0.001 TRP L 162 HIS 0.003 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5749) covalent geometry : angle 0.53786 ( 7817) SS BOND : bond 0.00312 ( 4) SS BOND : angle 0.60404 ( 8) hydrogen bonds : bond 0.03601 ( 319) hydrogen bonds : angle 4.25833 ( 915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.199 Fit side-chains REVERT: A 184 MET cc_start: 0.2454 (tmt) cc_final: 0.1897 (ttt) REVERT: A 196 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7625 (tm) REVERT: A 257 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8160 (tm-30) REVERT: L 107 ARG cc_start: 0.8085 (ptm160) cc_final: 0.7691 (ptm160) REVERT: L 174 MET cc_start: 0.8323 (tpt) cc_final: 0.7823 (tpt) REVERT: H 5 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7512 (tt0) outliers start: 27 outliers final: 23 residues processed: 101 average time/residue: 0.0589 time to fit residues: 8.5350 Evaluate side-chains 100 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.180853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.120291 restraints weight = 6170.629| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.19 r_work: 0.2858 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5753 Z= 0.150 Angle : 0.555 9.979 7825 Z= 0.279 Chirality : 0.041 0.148 908 Planarity : 0.005 0.048 965 Dihedral : 5.977 69.857 787 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.40 % Allowed : 27.00 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.78 (0.33), residues: 728 helix: 2.05 (0.32), residues: 266 sheet: 0.19 (0.36), residues: 221 loop : -0.85 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 252 TYR 0.028 0.001 TYR L 31 PHE 0.012 0.001 PHE H 107 TRP 0.015 0.001 TRP L 162 HIS 0.003 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 5749) covalent geometry : angle 0.55448 ( 7817) SS BOND : bond 0.00377 ( 4) SS BOND : angle 0.58336 ( 8) hydrogen bonds : bond 0.03773 ( 319) hydrogen bonds : angle 4.30536 ( 915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.170 Fit side-chains REVERT: A 184 MET cc_start: 0.2380 (tmt) cc_final: 0.1841 (ttt) REVERT: A 196 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7541 (tm) REVERT: A 256 MET cc_start: 0.8194 (mmm) cc_final: 0.7900 (mmm) REVERT: A 257 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8168 (tm-30) REVERT: L 107 ARG cc_start: 0.8051 (ptm160) cc_final: 0.7634 (ptm160) REVERT: L 174 MET cc_start: 0.8222 (tpt) cc_final: 0.7566 (tpt) REVERT: H 5 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7540 (tt0) outliers start: 28 outliers final: 23 residues processed: 101 average time/residue: 0.0544 time to fit residues: 7.8517 Evaluate side-chains 101 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.172344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.131465 restraints weight = 6002.830| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.62 r_work: 0.2817 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5753 Z= 0.138 Angle : 0.550 10.752 7825 Z= 0.278 Chirality : 0.041 0.154 908 Planarity : 0.005 0.048 965 Dihedral : 5.961 69.890 787 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.24 % Allowed : 27.16 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.78 (0.33), residues: 728 helix: 2.03 (0.32), residues: 266 sheet: 0.21 (0.35), residues: 223 loop : -0.87 (0.42), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.029 0.001 TYR L 31 PHE 0.011 0.001 PHE H 107 TRP 0.014 0.001 TRP L 162 HIS 0.003 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5749) covalent geometry : angle 0.55050 ( 7817) SS BOND : bond 0.00375 ( 4) SS BOND : angle 0.52328 ( 8) hydrogen bonds : bond 0.03687 ( 319) hydrogen bonds : angle 4.25802 ( 915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.156 Fit side-chains REVERT: A 184 MET cc_start: 0.2604 (tmt) cc_final: 0.2025 (ttt) REVERT: A 196 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7629 (tm) REVERT: A 257 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8100 (tm-30) REVERT: L 107 ARG cc_start: 0.8070 (ptm160) cc_final: 0.7641 (ptm160) REVERT: H 5 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7505 (tt0) outliers start: 27 outliers final: 22 residues processed: 99 average time/residue: 0.0561 time to fit residues: 7.9644 Evaluate side-chains 99 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 35 optimal weight: 0.0170 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.170929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.129597 restraints weight = 6083.044| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.69 r_work: 0.2861 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5753 Z= 0.105 Angle : 0.527 11.131 7825 Z= 0.265 Chirality : 0.040 0.144 908 Planarity : 0.005 0.048 965 Dihedral : 5.803 70.107 787 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.14 % Allowed : 28.57 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.88 (0.33), residues: 728 helix: 2.18 (0.33), residues: 266 sheet: 0.14 (0.35), residues: 229 loop : -0.78 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.025 0.001 TYR L 31 PHE 0.009 0.001 PHE H 107 TRP 0.012 0.001 TRP L 162 HIS 0.005 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 5749) covalent geometry : angle 0.52669 ( 7817) SS BOND : bond 0.00347 ( 4) SS BOND : angle 0.37148 ( 8) hydrogen bonds : bond 0.03195 ( 319) hydrogen bonds : angle 4.13009 ( 915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.167 Fit side-chains REVERT: A 196 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7600 (tm) REVERT: A 257 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8071 (tm-30) REVERT: L 107 ARG cc_start: 0.8034 (ptm160) cc_final: 0.7587 (ptm160) REVERT: L 174 MET cc_start: 0.8182 (tpt) cc_final: 0.7500 (tpt) REVERT: H 5 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7542 (tt0) outliers start: 20 outliers final: 16 residues processed: 95 average time/residue: 0.0554 time to fit residues: 7.4894 Evaluate side-chains 95 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 67 optimal weight: 0.0970 chunk 53 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.174484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.135536 restraints weight = 6146.045| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.47 r_work: 0.2940 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5753 Z= 0.134 Angle : 0.560 11.211 7825 Z= 0.279 Chirality : 0.041 0.146 908 Planarity : 0.005 0.047 965 Dihedral : 5.831 69.998 787 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.83 % Allowed : 29.36 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.84 (0.33), residues: 728 helix: 2.14 (0.33), residues: 266 sheet: 0.18 (0.35), residues: 227 loop : -0.87 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 252 TYR 0.027 0.001 TYR L 31 PHE 0.011 0.001 PHE H 107 TRP 0.013 0.001 TRP L 162 HIS 0.005 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5749) covalent geometry : angle 0.55974 ( 7817) SS BOND : bond 0.00339 ( 4) SS BOND : angle 0.40260 ( 8) hydrogen bonds : bond 0.03544 ( 319) hydrogen bonds : angle 4.19338 ( 915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.208 Fit side-chains REVERT: A 196 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7626 (tm) REVERT: A 257 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8096 (tm-30) REVERT: L 107 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7630 (ptm160) REVERT: L 174 MET cc_start: 0.8262 (tpt) cc_final: 0.7676 (tpt) REVERT: H 5 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7576 (tt0) outliers start: 18 outliers final: 15 residues processed: 93 average time/residue: 0.0598 time to fit residues: 7.9243 Evaluate side-chains 94 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 205 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.168981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.107086 restraints weight = 6109.333| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.99 r_work: 0.2891 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5753 Z= 0.128 Angle : 0.555 11.009 7825 Z= 0.275 Chirality : 0.040 0.144 908 Planarity : 0.005 0.047 965 Dihedral : 5.760 70.161 787 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.83 % Allowed : 28.73 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.83 (0.32), residues: 728 helix: 2.10 (0.32), residues: 266 sheet: 0.26 (0.35), residues: 223 loop : -0.91 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 252 TYR 0.032 0.001 TYR L 31 PHE 0.011 0.001 PHE H 107 TRP 0.012 0.001 TRP L 162 HIS 0.003 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5749) covalent geometry : angle 0.55465 ( 7817) SS BOND : bond 0.00317 ( 4) SS BOND : angle 0.48046 ( 8) hydrogen bonds : bond 0.03460 ( 319) hydrogen bonds : angle 4.19540 ( 915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1497.37 seconds wall clock time: 26 minutes 20.38 seconds (1580.38 seconds total)