Starting phenix.real_space_refine on Sat May 2 12:37:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11td_76031/05_2026/11td_76031.cif Found real_map, /net/cci-nas-00/data/ceres_data/11td_76031/05_2026/11td_76031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11td_76031/05_2026/11td_76031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11td_76031/05_2026/11td_76031.map" model { file = "/net/cci-nas-00/data/ceres_data/11td_76031/05_2026/11td_76031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11td_76031/05_2026/11td_76031.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 24 5.16 5 C 3237 2.51 5 N 807 2.21 5 O 901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4969 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3200 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 8, 'TRANS': 387} Chain breaks: 1 Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 949 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 1.47, per 1000 atoms: 0.30 Number of scatterers: 4969 At special positions: 0 Unit cell: (61.005, 86.73, 138.915, 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 24 16.00 O 901 8.00 N 807 7.00 C 3237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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: 0.35 Conformation dependent library (CDL) restraints added in 211.1 milliseconds 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 6 sheets defined 58.9% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'R' and resid 35 through 67 removed outlier: 3.542A pdb=" N PHE R 41 " --> pdb=" O PHE R 37 " (cutoff:3.500A) Proline residue: R 43 - end of helix Processing helix chain 'R' and resid 72 through 90 removed outlier: 3.562A pdb=" N VAL R 76 " --> pdb=" O SER R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 101 removed outlier: 3.648A pdb=" N TRP R 95 " --> pdb=" O SER R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 141 removed outlier: 3.723A pdb=" N HIS R 141 " --> pdb=" O LEU R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 148 Processing helix chain 'R' and resid 150 through 175 removed outlier: 3.553A pdb=" N THR R 157 " --> pdb=" O TYR R 153 " (cutoff:3.500A) Proline residue: R 171 - end of helix Processing helix chain 'R' and resid 195 through 255 removed outlier: 4.495A pdb=" N ILE R 213 " --> pdb=" O LEU R 209 " (cutoff:3.500A) Proline residue: R 214 - end of helix Processing helix chain 'R' and resid 258 through 279 removed outlier: 3.621A pdb=" N VAL R 262 " --> pdb=" O ASN R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 318 Processing helix chain 'R' and resid 320 through 385 removed outlier: 4.301A pdb=" N LYS R 340 " --> pdb=" O ALA R 336 " (cutoff:3.500A) Proline residue: R 372 - end of helix Processing helix chain 'R' and resid 390 through 420 Proline residue: R 416 - end of helix removed outlier: 3.543A pdb=" N PHE R 420 " --> pdb=" O PRO R 416 " (cutoff:3.500A) Processing helix chain 'R' and resid 426 through 440 Processing helix chain 'H' and resid 31 through 35 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.649A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 176 through 181 Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA3, first strand: chain 'H' and resid 14 through 15 removed outlier: 5.973A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.828A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.828A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN L 91 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1023 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: 0.70 Time building geometry restraints manager: 0.51 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: 1526 1.34 - 1.46: 1253 1.46 - 1.58: 2275 1.58 - 1.70: 0 1.70 - 1.81: 36 Bond restraints: 5090 Sorted by residual: bond pdb=" CB ILE R 139 " pdb=" CG2 ILE R 139 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 bond pdb=" CB GLU R 405 " pdb=" CG GLU R 405 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" N GLY R 423 " pdb=" CA GLY R 423 " ideal model delta sigma weight residual 1.458 1.448 0.010 9.20e-03 1.18e+04 1.17e+00 bond pdb=" CB ASP R 398 " pdb=" CG ASP R 398 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" CA GLN L 28 " pdb=" C GLN L 28 " ideal model delta sigma weight residual 1.532 1.521 0.011 1.12e-02 7.97e+03 9.86e-01 ... (remaining 5085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 6733 1.84 - 3.69: 138 3.69 - 5.53: 28 5.53 - 7.37: 5 7.37 - 9.22: 6 Bond angle restraints: 6910 Sorted by residual: angle pdb=" C GLN L 28 " pdb=" CA GLN L 28 " pdb=" CB GLN L 28 " ideal model delta sigma weight residual 116.34 110.43 5.91 1.40e+00 5.10e-01 1.78e+01 angle pdb=" C ALA R 138 " pdb=" N ILE R 139 " pdb=" CA ILE R 139 " ideal model delta sigma weight residual 122.35 117.98 4.37 1.18e+00 7.18e-01 1.37e+01 angle pdb=" C PHE R 65 " pdb=" N LYS R 66 " pdb=" CA LYS R 66 " ideal model delta sigma weight residual 122.36 117.44 4.92 1.72e+00 3.38e-01 8.19e+00 angle pdb=" C LYS R 111 " pdb=" N MET R 112 " pdb=" CA MET R 112 " ideal model delta sigma weight residual 121.14 116.40 4.74 1.75e+00 3.27e-01 7.34e+00 angle pdb=" CA LEU R 107 " pdb=" CB LEU R 107 " pdb=" CG LEU R 107 " ideal model delta sigma weight residual 116.30 125.52 -9.22 3.50e+00 8.16e-02 6.93e+00 ... (remaining 6905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2508 17.99 - 35.99: 350 35.99 - 53.98: 89 53.98 - 71.98: 22 71.98 - 89.97: 5 Dihedral angle restraints: 2974 sinusoidal: 1140 harmonic: 1834 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual -86.00 -57.04 -28.96 1 1.00e+01 1.00e-02 1.20e+01 dihedral pdb=" CA LEU R 211 " pdb=" C LEU R 211 " pdb=" N VAL R 212 " pdb=" CA VAL R 212 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA ASP H 115 " pdb=" CB ASP H 115 " pdb=" CG ASP H 115 " pdb=" OD1 ASP H 115 " ideal model delta sinusoidal sigma weight residual -30.00 -87.44 57.44 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 2971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 540 0.036 - 0.072: 174 0.072 - 0.108: 49 0.108 - 0.144: 17 0.144 - 0.180: 1 Chirality restraints: 781 Sorted by residual: chirality pdb=" CB THR R 245 " pdb=" CA THR R 245 " pdb=" OG1 THR R 245 " pdb=" CG2 THR R 245 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CG LEU R 204 " pdb=" CB LEU R 204 " pdb=" CD1 LEU R 204 " pdb=" CD2 LEU R 204 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CG LEU R 109 " pdb=" CB LEU R 109 " pdb=" CD1 LEU R 109 " pdb=" CD2 LEU R 109 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 778 not shown) Planarity restraints: 853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 50 " 0.014 2.00e-02 2.50e+03 1.31e-02 4.30e+00 pdb=" CG TRP H 50 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP H 50 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP H 50 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 50 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 50 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 50 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 50 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 50 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 335 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" C ASN R 335 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN R 335 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA R 336 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 42 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO R 43 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 43 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 43 " 0.021 5.00e-02 4.00e+02 ... (remaining 850 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 187 2.71 - 3.26: 5130 3.26 - 3.81: 8526 3.81 - 4.35: 9781 4.35 - 4.90: 16343 Nonbonded interactions: 39967 Sorted by model distance: nonbonded pdb=" OE1 GLU R 343 " pdb=" NH2 ARG R 346 " model vdw 2.166 3.120 nonbonded pdb=" NH2 ARG H 41 " pdb=" OE2 GLU H 49 " model vdw 2.207 3.120 nonbonded pdb=" OE2 GLU R 240 " pdb=" NH1 ARG R 346 " model vdw 2.213 3.120 nonbonded pdb=" OH TYR R 117 " pdb=" OE1 GLU R 405 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP H 76 " pdb=" OG1 THR H 81 " model vdw 2.238 3.040 ... (remaining 39962 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 group one per residue 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: 3.580 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.140 Find NCS groups from input model: 0.040 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 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 0.038 5093 Z= 0.168 Angle : 0.704 9.217 6916 Z= 0.366 Chirality : 0.041 0.180 781 Planarity : 0.004 0.038 853 Dihedral : 18.172 89.972 1789 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.75 % Allowed : 37.34 % Favored : 58.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.16 (0.34), residues: 619 helix: 1.71 (0.28), residues: 341 sheet: 1.02 (0.52), residues: 107 loop : -1.34 (0.44), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 298 TYR 0.017 0.002 TYR R 67 PHE 0.014 0.001 PHE R 105 TRP 0.036 0.002 TRP H 50 HIS 0.005 0.002 HIS R 141 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5090) covalent geometry : angle 0.70410 ( 6910) SS BOND : bond 0.00239 ( 3) SS BOND : angle 0.69484 ( 6) hydrogen bonds : bond 0.10772 ( 356) hydrogen bonds : angle 5.21586 ( 1023) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 116 MET cc_start: 0.7172 (tpp) cc_final: 0.6398 (tpt) REVERT: R 127 PHE cc_start: 0.8415 (m-80) cc_final: 0.7993 (m-80) REVERT: R 129 MET cc_start: 0.7374 (ptm) cc_final: 0.6818 (ptm) REVERT: R 131 MET cc_start: 0.7763 (ttp) cc_final: 0.7503 (ttm) REVERT: R 135 ARG cc_start: 0.8253 (tpp80) cc_final: 0.8043 (tpp80) REVERT: R 212 VAL cc_start: 0.8041 (m) cc_final: 0.7825 (t) REVERT: R 218 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7118 (mpp) REVERT: R 307 GLN cc_start: 0.7775 (mt0) cc_final: 0.7538 (mt0) REVERT: R 341 TYR cc_start: 0.7033 (t80) cc_final: 0.6494 (t80) REVERT: R 346 ARG cc_start: 0.7198 (ttp-110) cc_final: 0.6591 (ttp-110) REVERT: R 351 GLU cc_start: 0.7516 (pp20) cc_final: 0.7195 (pp20) REVERT: H 76 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.6074 (p0) REVERT: H 93 ASP cc_start: 0.8055 (m-30) cc_final: 0.7628 (m-30) REVERT: L 53 SER cc_start: 0.8317 (t) cc_final: 0.8111 (m) REVERT: L 80 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7452 (mp10) outliers start: 20 outliers final: 16 residues processed: 155 average time/residue: 0.0835 time to fit residues: 16.2892 Evaluate side-chains 160 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain R residue 301 PHE Chi-restraints excluded: chain R residue 309 ASP Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 350 ASN Chi-restraints excluded: chain R residue 414 LEU Chi-restraints excluded: chain R residue 425 LYS Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 324 GLN H 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.153476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122744 restraints weight = 8773.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126905 restraints weight = 4264.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129838 restraints weight = 2655.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.131383 restraints weight = 1905.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.132403 restraints weight = 1556.525| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5093 Z= 0.192 Angle : 0.639 7.959 6916 Z= 0.335 Chirality : 0.041 0.147 781 Planarity : 0.004 0.039 853 Dihedral : 8.652 58.533 725 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.75 % Allowed : 31.52 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.16 (0.34), residues: 619 helix: 1.80 (0.28), residues: 344 sheet: 0.91 (0.51), residues: 107 loop : -1.55 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 298 TYR 0.016 0.002 TYR R 67 PHE 0.012 0.001 PHE R 105 TRP 0.023 0.002 TRP H 50 HIS 0.005 0.002 HIS R 299 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 5090) covalent geometry : angle 0.63920 ( 6910) SS BOND : bond 0.00349 ( 3) SS BOND : angle 0.88600 ( 6) hydrogen bonds : bond 0.05173 ( 356) hydrogen bonds : angle 4.68266 ( 1023) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 62 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7773 (mm) REVERT: R 116 MET cc_start: 0.7309 (tpp) cc_final: 0.6496 (tpt) REVERT: R 129 MET cc_start: 0.7231 (ptm) cc_final: 0.6753 (ptm) REVERT: R 218 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7149 (mpp) REVERT: R 309 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: R 341 TYR cc_start: 0.7084 (t80) cc_final: 0.6479 (t80) REVERT: R 351 GLU cc_start: 0.7565 (pp20) cc_final: 0.7201 (pp20) REVERT: R 369 PHE cc_start: 0.7438 (m-80) cc_final: 0.6827 (t80) REVERT: R 398 ASP cc_start: 0.7572 (p0) cc_final: 0.7268 (t0) REVERT: R 433 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.4713 (mt) REVERT: H 93 ASP cc_start: 0.8182 (m-30) cc_final: 0.7670 (m-30) REVERT: L 53 SER cc_start: 0.8322 (t) cc_final: 0.8120 (m) REVERT: L 79 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7714 (tp) REVERT: L 80 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7619 (mp10) outliers start: 36 outliers final: 22 residues processed: 168 average time/residue: 0.0765 time to fit residues: 16.4246 Evaluate side-chains 166 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 105 PHE Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 278 LYS Chi-restraints excluded: chain R residue 301 PHE Chi-restraints excluded: chain R residue 309 ASP Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain R residue 350 ASN Chi-restraints excluded: chain R residue 425 LYS Chi-restraints excluded: chain R residue 433 LEU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 0.0050 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 324 GLN H 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.151553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120736 restraints weight = 8786.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124886 restraints weight = 4277.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127823 restraints weight = 2691.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.129503 restraints weight = 1942.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.130219 restraints weight = 1565.470| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5093 Z= 0.226 Angle : 0.665 9.858 6916 Z= 0.348 Chirality : 0.042 0.154 781 Planarity : 0.004 0.039 853 Dihedral : 7.885 58.497 711 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 9.01 % Allowed : 30.58 % Favored : 60.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.98 (0.33), residues: 619 helix: 1.69 (0.27), residues: 345 sheet: 0.76 (0.51), residues: 107 loop : -1.66 (0.42), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 41 TYR 0.023 0.002 TYR R 67 PHE 0.015 0.001 PHE R 105 TRP 0.025 0.002 TRP H 50 HIS 0.005 0.002 HIS R 141 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 5090) covalent geometry : angle 0.66423 ( 6910) SS BOND : bond 0.00450 ( 3) SS BOND : angle 1.37836 ( 6) hydrogen bonds : bond 0.05599 ( 356) hydrogen bonds : angle 4.76984 ( 1023) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: R 62 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7706 (mm) REVERT: R 78 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.6466 (tp) REVERT: R 84 SER cc_start: 0.7759 (OUTLIER) cc_final: 0.7547 (t) REVERT: R 116 MET cc_start: 0.7492 (tpp) cc_final: 0.7019 (tpp) REVERT: R 129 MET cc_start: 0.7207 (ptm) cc_final: 0.6714 (ptm) REVERT: R 220 PHE cc_start: 0.7336 (t80) cc_final: 0.7019 (t80) REVERT: R 249 ASN cc_start: 0.7536 (m-40) cc_final: 0.7166 (m-40) REVERT: R 329 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7303 (mm-40) REVERT: R 331 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6788 (tptp) REVERT: R 398 ASP cc_start: 0.7701 (p0) cc_final: 0.7397 (t0) REVERT: R 433 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.5022 (mt) REVERT: H 93 ASP cc_start: 0.8197 (m-30) cc_final: 0.7744 (m-30) REVERT: L 79 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7694 (tp) REVERT: L 80 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7685 (mp10) outliers start: 48 outliers final: 31 residues processed: 171 average time/residue: 0.0778 time to fit residues: 16.8101 Evaluate side-chains 178 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 105 PHE Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 186 TYR Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 278 LYS Chi-restraints excluded: chain R residue 301 PHE Chi-restraints excluded: chain R residue 331 LYS Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 350 ASN Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 425 LYS Chi-restraints excluded: chain R residue 433 LEU Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.0070 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 247 ASN ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.154587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123963 restraints weight = 8776.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.128221 restraints weight = 4296.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.131120 restraints weight = 2677.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132889 restraints weight = 1926.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133658 restraints weight = 1545.600| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5093 Z= 0.157 Angle : 0.637 7.711 6916 Z= 0.332 Chirality : 0.040 0.153 781 Planarity : 0.004 0.042 853 Dihedral : 7.105 58.705 706 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 8.07 % Allowed : 29.83 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.17 (0.33), residues: 619 helix: 1.89 (0.27), residues: 342 sheet: 0.78 (0.51), residues: 107 loop : -1.60 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 427 TYR 0.029 0.002 TYR R 67 PHE 0.016 0.001 PHE R 297 TRP 0.024 0.001 TRP H 50 HIS 0.004 0.001 HIS R 141 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5090) covalent geometry : angle 0.63664 ( 6910) SS BOND : bond 0.00336 ( 3) SS BOND : angle 0.94842 ( 6) hydrogen bonds : bond 0.05062 ( 356) hydrogen bonds : angle 4.56823 ( 1023) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 84 SER cc_start: 0.7705 (OUTLIER) cc_final: 0.7492 (t) REVERT: R 116 MET cc_start: 0.7487 (tpp) cc_final: 0.6991 (tpp) REVERT: R 117 TYR cc_start: 0.7777 (t80) cc_final: 0.6688 (t80) REVERT: R 129 MET cc_start: 0.7029 (ptm) cc_final: 0.6622 (ptm) REVERT: R 130 LEU cc_start: 0.7635 (mt) cc_final: 0.7426 (mt) REVERT: R 170 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7014 (mt) REVERT: R 217 ILE cc_start: 0.7869 (pt) cc_final: 0.7508 (pt) REVERT: R 220 PHE cc_start: 0.7312 (t80) cc_final: 0.6981 (t80) REVERT: R 249 ASN cc_start: 0.7538 (m-40) cc_final: 0.7165 (m-40) REVERT: R 329 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7271 (mm-40) REVERT: R 331 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6722 (tptp) REVERT: R 350 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7475 (p0) REVERT: R 351 GLU cc_start: 0.7524 (pp20) cc_final: 0.7158 (pp20) REVERT: R 398 ASP cc_start: 0.7688 (p0) cc_final: 0.7408 (t0) REVERT: H 39 TRP cc_start: 0.8218 (m100) cc_final: 0.7916 (m100) REVERT: H 76 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6530 (p0) REVERT: H 93 ASP cc_start: 0.8141 (m-30) cc_final: 0.7695 (m-30) REVERT: L 79 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7642 (tp) REVERT: L 80 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7762 (mp10) outliers start: 43 outliers final: 29 residues processed: 184 average time/residue: 0.0772 time to fit residues: 18.0233 Evaluate side-chains 188 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 186 TYR Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 264 ASP Chi-restraints excluded: chain R residue 278 LYS Chi-restraints excluded: chain R residue 301 PHE Chi-restraints excluded: chain R residue 331 LYS Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 350 ASN Chi-restraints excluded: chain R residue 425 LYS Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 141 HIS ** R 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.154824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124042 restraints weight = 8749.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128210 restraints weight = 4318.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.131033 restraints weight = 2705.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132781 restraints weight = 1962.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133686 restraints weight = 1578.642| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5093 Z= 0.166 Angle : 0.631 7.408 6916 Z= 0.331 Chirality : 0.040 0.168 781 Planarity : 0.004 0.042 853 Dihedral : 7.101 59.624 706 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 7.88 % Allowed : 31.14 % Favored : 60.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.22 (0.34), residues: 619 helix: 1.93 (0.27), residues: 343 sheet: 0.76 (0.51), residues: 107 loop : -1.58 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 41 TYR 0.021 0.002 TYR R 67 PHE 0.012 0.001 PHE R 173 TRP 0.024 0.001 TRP H 50 HIS 0.006 0.002 HIS R 184 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5090) covalent geometry : angle 0.63110 ( 6910) SS BOND : bond 0.00352 ( 3) SS BOND : angle 0.75501 ( 6) hydrogen bonds : bond 0.05058 ( 356) hydrogen bonds : angle 4.58054 ( 1023) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 62 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7572 (mm) REVERT: R 95 TRP cc_start: 0.7608 (m100) cc_final: 0.7233 (m100) REVERT: R 98 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: R 116 MET cc_start: 0.7525 (tpp) cc_final: 0.7061 (tpp) REVERT: R 129 MET cc_start: 0.7095 (ptm) cc_final: 0.6667 (ptm) REVERT: R 170 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7060 (mt) REVERT: R 217 ILE cc_start: 0.7764 (pt) cc_final: 0.7466 (pt) REVERT: R 220 PHE cc_start: 0.7331 (t80) cc_final: 0.6981 (t80) REVERT: R 249 ASN cc_start: 0.7523 (m-40) cc_final: 0.7182 (m-40) REVERT: R 329 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7328 (mm-40) REVERT: R 331 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6710 (tptp) REVERT: R 346 ARG cc_start: 0.7475 (ttp-110) cc_final: 0.7159 (ttp-110) REVERT: R 350 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7464 (p0) REVERT: R 351 GLU cc_start: 0.7528 (pp20) cc_final: 0.7179 (pp20) REVERT: H 39 TRP cc_start: 0.8203 (m100) cc_final: 0.7964 (m100) REVERT: H 93 ASP cc_start: 0.8157 (m-30) cc_final: 0.7715 (m-30) REVERT: L 80 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7739 (mp10) outliers start: 42 outliers final: 28 residues processed: 177 average time/residue: 0.0744 time to fit residues: 16.6637 Evaluate side-chains 184 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 98 TYR Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 186 TYR Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 301 PHE Chi-restraints excluded: chain R residue 331 LYS Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 350 ASN Chi-restraints excluded: chain R residue 425 LYS Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 109 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 22 optimal weight: 0.0000 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 HIS ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.153451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122735 restraints weight = 8842.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126960 restraints weight = 4354.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129821 restraints weight = 2716.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.131403 restraints weight = 1959.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.132240 restraints weight = 1594.967| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5093 Z= 0.199 Angle : 0.680 11.383 6916 Z= 0.352 Chirality : 0.042 0.171 781 Planarity : 0.004 0.042 853 Dihedral : 7.046 59.724 704 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 7.50 % Allowed : 32.08 % Favored : 60.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.13 (0.34), residues: 619 helix: 1.82 (0.27), residues: 345 sheet: 0.70 (0.52), residues: 107 loop : -1.54 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 41 TYR 0.020 0.002 TYR R 67 PHE 0.015 0.001 PHE R 297 TRP 0.021 0.001 TRP H 50 HIS 0.004 0.001 HIS R 184 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 5090) covalent geometry : angle 0.68013 ( 6910) SS BOND : bond 0.00700 ( 3) SS BOND : angle 1.00241 ( 6) hydrogen bonds : bond 0.05233 ( 356) hydrogen bonds : angle 4.65863 ( 1023) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: R 116 MET cc_start: 0.7525 (tpp) cc_final: 0.7084 (tpp) REVERT: R 129 MET cc_start: 0.7055 (ptm) cc_final: 0.6646 (ptm) REVERT: R 170 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7002 (mt) REVERT: R 218 MET cc_start: 0.7799 (mtp) cc_final: 0.7461 (mtp) REVERT: R 220 PHE cc_start: 0.7370 (t80) cc_final: 0.7025 (t80) REVERT: R 249 ASN cc_start: 0.7573 (m-40) cc_final: 0.7135 (m-40) REVERT: R 269 MET cc_start: 0.7491 (mtm) cc_final: 0.7289 (mtp) REVERT: R 329 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7356 (mm-40) REVERT: R 331 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6844 (tptp) REVERT: R 346 ARG cc_start: 0.7492 (ttp-110) cc_final: 0.7212 (ttp-110) REVERT: R 350 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7480 (p0) REVERT: R 351 GLU cc_start: 0.7561 (pp20) cc_final: 0.7203 (pp20) REVERT: R 380 GLU cc_start: 0.7058 (tp30) cc_final: 0.6724 (tp30) REVERT: H 39 TRP cc_start: 0.8211 (m100) cc_final: 0.7979 (m100) REVERT: H 93 ASP cc_start: 0.8136 (m-30) cc_final: 0.7716 (m-30) REVERT: L 80 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7746 (mp10) outliers start: 40 outliers final: 26 residues processed: 167 average time/residue: 0.0766 time to fit residues: 16.2068 Evaluate side-chains 173 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 98 TYR Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 186 TYR Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 301 PHE Chi-restraints excluded: chain R residue 331 LYS Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain R residue 350 ASN Chi-restraints excluded: chain R residue 414 LEU Chi-restraints excluded: chain R residue 425 LYS Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 109 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.0670 chunk 40 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.154602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.123746 restraints weight = 8805.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.128040 restraints weight = 4314.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.130857 restraints weight = 2695.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.132717 restraints weight = 1963.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.133545 restraints weight = 1575.197| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5093 Z= 0.169 Angle : 0.655 10.154 6916 Z= 0.340 Chirality : 0.041 0.173 781 Planarity : 0.004 0.043 853 Dihedral : 7.008 59.083 704 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 7.50 % Allowed : 32.46 % Favored : 60.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.18 (0.34), residues: 619 helix: 1.87 (0.27), residues: 345 sheet: 0.67 (0.52), residues: 107 loop : -1.49 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 41 TYR 0.019 0.002 TYR R 67 PHE 0.019 0.001 PHE R 297 TRP 0.026 0.001 TRP H 50 HIS 0.002 0.001 HIS R 299 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5090) covalent geometry : angle 0.65449 ( 6910) SS BOND : bond 0.00547 ( 3) SS BOND : angle 0.94835 ( 6) hydrogen bonds : bond 0.05032 ( 356) hydrogen bonds : angle 4.58644 ( 1023) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: R 98 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: R 115 TRP cc_start: 0.7102 (t60) cc_final: 0.6780 (t60) REVERT: R 116 MET cc_start: 0.7545 (tpp) cc_final: 0.6405 (tpp) REVERT: R 129 MET cc_start: 0.6978 (ptm) cc_final: 0.6622 (ptm) REVERT: R 170 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6931 (mt) REVERT: R 181 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5997 (tm-30) REVERT: R 220 PHE cc_start: 0.7344 (t80) cc_final: 0.6990 (t80) REVERT: R 240 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6765 (mm-30) REVERT: R 246 LEU cc_start: 0.8545 (mt) cc_final: 0.7946 (mt) REVERT: R 249 ASN cc_start: 0.7575 (m-40) cc_final: 0.7136 (m-40) REVERT: R 329 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7327 (mm-40) REVERT: R 331 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6843 (tptp) REVERT: R 346 ARG cc_start: 0.7471 (ttp-110) cc_final: 0.7126 (ttp-110) REVERT: R 350 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7463 (p0) REVERT: R 351 GLU cc_start: 0.7563 (pp20) cc_final: 0.7220 (pp20) REVERT: R 380 GLU cc_start: 0.7003 (tp30) cc_final: 0.6707 (tp30) REVERT: R 427 ARG cc_start: 0.7074 (ttm-80) cc_final: 0.6636 (ttm-80) REVERT: H 39 TRP cc_start: 0.8176 (m100) cc_final: 0.7938 (m100) REVERT: H 76 ASP cc_start: 0.7092 (p0) cc_final: 0.6631 (p0) REVERT: H 93 ASP cc_start: 0.8126 (m-30) cc_final: 0.7714 (m-30) REVERT: L 80 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7661 (mp10) outliers start: 40 outliers final: 31 residues processed: 170 average time/residue: 0.0730 time to fit residues: 15.8702 Evaluate side-chains 179 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 98 TYR Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 186 TYR Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 264 ASP Chi-restraints excluded: chain R residue 301 PHE Chi-restraints excluded: chain R residue 331 LYS Chi-restraints excluded: chain R residue 332 THR Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 350 ASN Chi-restraints excluded: chain R residue 425 LYS Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 109 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.0020 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.154968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124152 restraints weight = 8768.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128458 restraints weight = 4310.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.131127 restraints weight = 2692.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.133015 restraints weight = 1978.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.133617 restraints weight = 1588.790| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5093 Z= 0.161 Angle : 0.673 10.567 6916 Z= 0.345 Chirality : 0.041 0.180 781 Planarity : 0.004 0.043 853 Dihedral : 7.003 59.646 704 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.57 % Allowed : 34.15 % Favored : 59.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.20 (0.34), residues: 619 helix: 1.88 (0.27), residues: 345 sheet: 0.77 (0.52), residues: 105 loop : -1.50 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 41 TYR 0.031 0.002 TYR R 67 PHE 0.023 0.001 PHE R 297 TRP 0.024 0.001 TRP H 50 HIS 0.003 0.001 HIS R 411 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5090) covalent geometry : angle 0.67241 ( 6910) SS BOND : bond 0.00550 ( 3) SS BOND : angle 1.06256 ( 6) hydrogen bonds : bond 0.04984 ( 356) hydrogen bonds : angle 4.54691 ( 1023) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: R 98 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: R 115 TRP cc_start: 0.7116 (t60) cc_final: 0.6885 (t60) REVERT: R 129 MET cc_start: 0.6985 (ptm) cc_final: 0.6532 (ptm) REVERT: R 170 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6887 (mt) REVERT: R 181 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6006 (tm-30) REVERT: R 220 PHE cc_start: 0.7328 (t80) cc_final: 0.6975 (t80) REVERT: R 240 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6751 (mm-30) REVERT: R 249 ASN cc_start: 0.7528 (m-40) cc_final: 0.7144 (m-40) REVERT: R 329 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7336 (mm-40) REVERT: R 331 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6763 (tptp) REVERT: R 346 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.7121 (ttp-110) REVERT: R 350 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7445 (p0) REVERT: R 351 GLU cc_start: 0.7550 (pp20) cc_final: 0.7197 (pp20) REVERT: R 380 GLU cc_start: 0.7013 (tp30) cc_final: 0.6716 (tp30) REVERT: R 427 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6622 (ttm-80) REVERT: H 39 TRP cc_start: 0.8172 (m100) cc_final: 0.7964 (m100) REVERT: H 76 ASP cc_start: 0.7096 (p0) cc_final: 0.6647 (p0) REVERT: H 85 GLN cc_start: 0.7339 (tp-100) cc_final: 0.7085 (tp40) REVERT: H 93 ASP cc_start: 0.8118 (m-30) cc_final: 0.7712 (m-30) REVERT: L 80 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7709 (mp10) outliers start: 35 outliers final: 26 residues processed: 165 average time/residue: 0.0710 time to fit residues: 15.0911 Evaluate side-chains 177 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 98 TYR Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 186 TYR Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 301 PHE Chi-restraints excluded: chain R residue 331 LYS Chi-restraints excluded: chain R residue 350 ASN Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 425 LYS Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 109 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 59 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 207 ASN ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.153368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122675 restraints weight = 8684.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126857 restraints weight = 4281.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129696 restraints weight = 2675.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.131399 restraints weight = 1951.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.132127 restraints weight = 1574.104| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5093 Z= 0.193 Angle : 0.689 10.899 6916 Z= 0.354 Chirality : 0.042 0.178 781 Planarity : 0.004 0.043 853 Dihedral : 7.011 58.528 703 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 6.38 % Allowed : 34.15 % Favored : 59.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.13 (0.34), residues: 619 helix: 1.81 (0.27), residues: 345 sheet: 0.59 (0.51), residues: 112 loop : -1.49 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 41 TYR 0.018 0.002 TYR R 98 PHE 0.024 0.001 PHE R 297 TRP 0.024 0.002 TRP H 50 HIS 0.004 0.001 HIS R 411 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 5090) covalent geometry : angle 0.68884 ( 6910) SS BOND : bond 0.00606 ( 3) SS BOND : angle 1.08571 ( 6) hydrogen bonds : bond 0.05250 ( 356) hydrogen bonds : angle 4.66997 ( 1023) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: R 115 TRP cc_start: 0.7143 (t60) cc_final: 0.6842 (t60) REVERT: R 116 MET cc_start: 0.7607 (tpp) cc_final: 0.6509 (tpp) REVERT: R 129 MET cc_start: 0.6939 (ptm) cc_final: 0.6532 (ptm) REVERT: R 170 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6877 (mt) REVERT: R 220 PHE cc_start: 0.7290 (t80) cc_final: 0.6916 (t80) REVERT: R 240 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6809 (mm-30) REVERT: R 307 GLN cc_start: 0.7763 (mt0) cc_final: 0.7552 (mt0) REVERT: R 329 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7429 (mm-40) REVERT: R 346 ARG cc_start: 0.7511 (ttp-110) cc_final: 0.7213 (ttp-110) REVERT: R 350 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7499 (p0) REVERT: R 351 GLU cc_start: 0.7575 (pp20) cc_final: 0.7201 (pp20) REVERT: R 380 GLU cc_start: 0.7064 (tp30) cc_final: 0.6735 (tp30) REVERT: R 394 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7306 (mt-10) REVERT: H 39 TRP cc_start: 0.8185 (m100) cc_final: 0.7959 (m100) REVERT: H 76 ASP cc_start: 0.7105 (p0) cc_final: 0.6676 (p0) REVERT: H 93 ASP cc_start: 0.8092 (m-30) cc_final: 0.7707 (m-30) REVERT: L 80 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7779 (mp10) outliers start: 34 outliers final: 27 residues processed: 166 average time/residue: 0.0743 time to fit residues: 15.7509 Evaluate side-chains 179 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 98 TYR Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 186 TYR Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 207 ASN Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 301 PHE Chi-restraints excluded: chain R residue 350 ASN Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 425 LYS Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 109 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 0.5980 chunk 22 optimal weight: 0.0570 chunk 56 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 207 ASN ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.153683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.123306 restraints weight = 8737.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.127487 restraints weight = 4266.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.130176 restraints weight = 2665.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.132115 restraints weight = 1945.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.133124 restraints weight = 1549.843| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5093 Z= 0.172 Angle : 0.700 10.714 6916 Z= 0.359 Chirality : 0.042 0.190 781 Planarity : 0.004 0.043 853 Dihedral : 6.896 55.999 703 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.19 % Allowed : 35.08 % Favored : 58.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.21 (0.34), residues: 619 helix: 1.83 (0.27), residues: 345 sheet: 0.82 (0.53), residues: 106 loop : -1.43 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 346 TYR 0.019 0.002 TYR R 419 PHE 0.031 0.001 PHE R 297 TRP 0.033 0.001 TRP H 50 HIS 0.003 0.001 HIS R 411 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 5090) covalent geometry : angle 0.70024 ( 6910) SS BOND : bond 0.00526 ( 3) SS BOND : angle 0.88373 ( 6) hydrogen bonds : bond 0.05106 ( 356) hydrogen bonds : angle 4.62139 ( 1023) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: R 115 TRP cc_start: 0.7134 (t60) cc_final: 0.6837 (t60) REVERT: R 116 MET cc_start: 0.7606 (tpp) cc_final: 0.6524 (tpp) REVERT: R 127 PHE cc_start: 0.8549 (m-80) cc_final: 0.7894 (m-80) REVERT: R 129 MET cc_start: 0.6951 (ptm) cc_final: 0.6509 (ptm) REVERT: R 170 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6883 (mt) REVERT: R 220 PHE cc_start: 0.7299 (t80) cc_final: 0.6928 (t80) REVERT: R 240 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: R 249 ASN cc_start: 0.7454 (m-40) cc_final: 0.7064 (m-40) REVERT: R 329 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7407 (mm-40) REVERT: R 346 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.7206 (ttp-110) REVERT: R 350 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7479 (p0) REVERT: R 351 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7176 (pp20) REVERT: R 394 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7289 (mt-10) REVERT: H 39 TRP cc_start: 0.8176 (m100) cc_final: 0.7958 (m100) REVERT: H 76 ASP cc_start: 0.7076 (p0) cc_final: 0.6565 (p0) REVERT: H 85 GLN cc_start: 0.7381 (tp-100) cc_final: 0.7158 (tp40) REVERT: H 93 ASP cc_start: 0.8089 (m-30) cc_final: 0.7690 (m-30) REVERT: L 80 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7802 (mp10) outliers start: 33 outliers final: 27 residues processed: 162 average time/residue: 0.0695 time to fit residues: 14.5906 Evaluate side-chains 180 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 98 TYR Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 186 TYR Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 207 ASN Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain R residue 301 PHE Chi-restraints excluded: chain R residue 350 ASN Chi-restraints excluded: chain R residue 351 GLU Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 425 LYS Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 109 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 207 ASN ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.153397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122553 restraints weight = 8893.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.126860 restraints weight = 4346.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129400 restraints weight = 2709.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131502 restraints weight = 2000.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.132329 restraints weight = 1587.899| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 5093 Z= 0.239 Angle : 1.138 59.181 6916 Z= 0.673 Chirality : 0.046 0.439 781 Planarity : 0.005 0.060 853 Dihedral : 6.957 55.999 703 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.38 % Allowed : 35.65 % Favored : 57.97 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 5.88 % 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: 1.12 (0.34), residues: 619 helix: 1.79 (0.27), residues: 345 sheet: 0.61 (0.52), residues: 112 loop : -1.46 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 346 TYR 0.019 0.002 TYR R 67 PHE 0.025 0.001 PHE R 297 TRP 0.030 0.001 TRP H 50 HIS 0.003 0.001 HIS R 411 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 5090) covalent geometry : angle 1.13821 ( 6910) SS BOND : bond 0.00526 ( 3) SS BOND : angle 0.86281 ( 6) hydrogen bonds : bond 0.05198 ( 356) hydrogen bonds : angle 4.65470 ( 1023) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1189.72 seconds wall clock time: 21 minutes 11.47 seconds (1271.47 seconds total)