Starting phenix.real_space_refine on Wed Jul 1 23:16:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ymh_33928/07_2026/7ymh_33928.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymh_33928/07_2026/7ymh_33928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ymh_33928/07_2026/7ymh_33928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymh_33928/07_2026/7ymh_33928.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ymh_33928/07_2026/7ymh_33928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymh_33928/07_2026/7ymh_33928.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ymh_33928/07_2026/7ymh_33928.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ymh_33928/07_2026/7ymh_33928.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.051 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 2577 2.51 5 N 657 2.21 5 O 690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3948 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2038 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 14, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 1389 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 197, 1384 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 9, 'ASP:plan': 9, 'ASN:plan1': 4, 'GLU:plan': 11, 'TRP:plan': 2, 'GLN:plan1': 3, 'PHE:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 183 Conformer: "B" Number of residues, atoms: 197, 1384 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 9, 'ASP:plan': 9, 'ASN:plan1': 4, 'GLU:plan': 11, 'TRP:plan': 2, 'GLN:plan1': 3, 'PHE:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 183 bond proxies already assigned to first conformer: 1403 Chain: "D" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 509 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'GLU:plan': 2, 'TYR:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA B 158 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA B 158 " occ=0.50 Time building chain proxies: 1.30, per 1000 atoms: 0.33 Number of scatterers: 3948 At special positions: 0 Unit cell: (58.1887, 61.4824, 139.433, 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 690 8.00 N 657 7.00 C 2577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 176 " 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: 0.32 Conformation dependent library (CDL) restraints added in 209.3 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1026 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 4 sheets defined 53.9% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 26 through 50 Processing helix chain 'A' and resid 59 through 90 removed outlier: 3.636A pdb=" N LEU A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 96 through 129 removed outlier: 3.719A pdb=" N ALA A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 160 through 163 removed outlier: 3.734A pdb=" N PHE A 163 " --> pdb=" O GLY A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 183 through 191 removed outlier: 3.889A pdb=" N PHE A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 211 Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.915A pdb=" N LYS A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 298 removed outlier: 4.635A pdb=" N PHE A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Proline residue: A 287 - end of helix Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 304 through 329 removed outlier: 3.946A pdb=" N GLY A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Proline residue: A 323 - end of helix removed outlier: 3.576A pdb=" N TYR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.556A pdb=" N LYS B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 removed outlier: 4.380A pdb=" N GLN B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 127 through 136 removed outlier: 3.605A pdb=" N GLU B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 165 through 184 Processing helix chain 'B' and resid 205 through 225 Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 20 Processing sheet with id=AA2, first strand: chain 'B' and resid 88 through 93 Processing sheet with id=AA3, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.275A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL D 91 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 66 through 69 224 hydrogen bonds defined for protein. 663 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: 0.55 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1232 1.34 - 1.46: 961 1.46 - 1.58: 1813 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4037 Sorted by residual: bond pdb=" CAJ E5E A 401 " pdb=" OAC E5E A 401 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" CAI E5E A 401 " pdb=" OAB E5E A 401 " ideal model delta sigma weight residual 1.354 1.400 -0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 1.469 1.482 -0.013 7.40e-03 1.83e+04 3.25e+00 bond pdb=" CAH E5E A 401 " pdb=" NAA E5E A 401 " ideal model delta sigma weight residual 1.486 1.451 0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C LEU A 80 " pdb=" N PRO A 81 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.47e+00 ... (remaining 4032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 5268 1.60 - 3.21: 204 3.21 - 4.81: 38 4.81 - 6.41: 10 6.41 - 8.02: 4 Bond angle restraints: 5524 Sorted by residual: angle pdb=" N ILE A 159 " pdb=" CA ILE A 159 " pdb=" C ILE A 159 " ideal model delta sigma weight residual 111.91 106.40 5.51 8.90e-01 1.26e+00 3.83e+01 angle pdb=" N ASP A 300 " pdb=" CA ASP A 300 " pdb=" C ASP A 300 " ideal model delta sigma weight residual 114.31 108.59 5.72 1.29e+00 6.01e-01 1.97e+01 angle pdb=" N ILE A 178 " pdb=" CA ILE A 178 " pdb=" C ILE A 178 " ideal model delta sigma weight residual 110.05 106.05 4.00 1.09e+00 8.42e-01 1.35e+01 angle pdb=" C ILE A 321 " pdb=" N ASN A 322 " pdb=" CA ASN A 322 " ideal model delta sigma weight residual 120.06 124.17 -4.11 1.19e+00 7.06e-01 1.19e+01 angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 109.81 116.27 -6.46 2.21e+00 2.05e-01 8.54e+00 ... (remaining 5519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 2059 15.48 - 30.95: 207 30.95 - 46.43: 49 46.43 - 61.90: 4 61.90 - 77.38: 4 Dihedral angle restraints: 2323 sinusoidal: 738 harmonic: 1585 Sorted by residual: dihedral pdb=" CA PRO A 161 " pdb=" C PRO A 161 " pdb=" N LEU A 162 " pdb=" CA LEU A 162 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ILE A 325 " pdb=" C ILE A 325 " pdb=" N TYR A 326 " pdb=" CA TYR A 326 " ideal model delta harmonic sigma weight residual -180.00 -160.88 -19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PHE A 193 " pdb=" C PHE A 193 " pdb=" N TYR A 194 " pdb=" CA TYR A 194 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 2320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 393 0.038 - 0.075: 190 0.075 - 0.113: 56 0.113 - 0.151: 21 0.151 - 0.189: 6 Chirality restraints: 666 Sorted by residual: chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CAL E5E A 401 " pdb=" CAH E5E A 401 " pdb=" CAK E5E A 401 " pdb=" OAD E5E A 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.49 0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA TYR A 326 " pdb=" N TYR A 326 " pdb=" C TYR A 326 " pdb=" CB TYR A 326 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 663 not shown) Planarity restraints: 688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 322 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO A 323 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 326 " 0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO A 327 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 286 " -0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 287 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " -0.034 5.00e-02 4.00e+02 ... (remaining 685 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1341 2.84 - 3.35: 3524 3.35 - 3.87: 6319 3.87 - 4.38: 6842 4.38 - 4.90: 12224 Nonbonded interactions: 30250 Sorted by model distance: nonbonded pdb=" OH TYR B 194 " pdb=" OD2 ASP B 215 " model vdw 2.324 3.040 nonbonded pdb=" OD1 ASP A 172 " pdb=" OH TYR D 37 " model vdw 2.331 3.040 nonbonded pdb=" OG SER D 69 " pdb=" O TYR D 78 " model vdw 2.383 3.040 nonbonded pdb=" O THR A 139 " pdb=" N GLY A 143 " model vdw 2.383 3.120 nonbonded pdb=" O ASP A 72 " pdb=" OG1 THR A 76 " model vdw 2.417 3.040 ... (remaining 30245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.780 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.850 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4038 Z= 0.204 Angle : 0.780 8.018 5526 Z= 0.448 Chirality : 0.050 0.189 666 Planarity : 0.007 0.075 688 Dihedral : 13.784 77.379 1294 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.28), residues: 527 helix: -2.63 (0.23), residues: 283 sheet: -3.00 (0.49), residues: 67 loop : -3.32 (0.39), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 207 TYR 0.018 0.001 TYR A 134 PHE 0.012 0.002 PHE A 308 TRP 0.009 0.002 TRP B 111 HIS 0.006 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 ( 4037) covalent geometry : angle 0.77982 / 0.45 ( 5524) SS BOND : bond 0.00295 / 0.16 ( 1) SS BOND : angle 0.61919 / 0.34 ( 2) hydrogen bonds : bond 0.13040 / 8.76 ( 224) hydrogen bonds : angle 6.89403 / 4.98 ( 663) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8592 (mp) cc_final: 0.8371 (mp) REVERT: A 165 TRP cc_start: 0.4361 (m100) cc_final: 0.4151 (m100) REVERT: A 272 LYS cc_start: 0.8785 (tppp) cc_final: 0.8292 (tptt) REVERT: B 215 ASP cc_start: 0.8500 (t70) cc_final: 0.7595 (t0) REVERT: D 100 TYR cc_start: 0.8228 (p90) cc_final: 0.7856 (p90) REVERT: D 102 ASP cc_start: 0.8443 (t70) cc_final: 0.7816 (t70) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0744 time to fit residues: 10.4456 Evaluate side-chains 87 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN A 331 GLN B 16 HIS ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108160 restraints weight = 6149.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108928 restraints weight = 3633.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110912 restraints weight = 2914.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111178 restraints weight = 2257.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112009 restraints weight = 2156.171| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4038 Z= 0.135 Angle : 0.560 6.061 5526 Z= 0.303 Chirality : 0.041 0.128 666 Planarity : 0.005 0.042 688 Dihedral : 4.418 18.314 577 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.63 % Allowed : 15.26 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.33), residues: 527 helix: -0.75 (0.29), residues: 282 sheet: -2.46 (0.54), residues: 67 loop : -2.93 (0.39), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 176 TYR 0.013 0.001 TYR A 326 PHE 0.008 0.001 PHE B 107 TRP 0.009 0.001 TRP A 102 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 4037) covalent geometry : angle 0.55962 / 0.30 ( 5524) SS BOND : bond 0.00285 / 0.15 ( 1) SS BOND : angle 0.37031 / 0.20 ( 2) hydrogen bonds : bond 0.04404 / 3.23 ( 224) hydrogen bonds : angle 4.73119 / 3.42 ( 663) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8060 (mtp) cc_final: 0.7661 (mtt) REVERT: A 165 TRP cc_start: 0.4223 (m100) cc_final: 0.3809 (m100) REVERT: A 272 LYS cc_start: 0.8725 (tppp) cc_final: 0.8220 (tptt) REVERT: B 215 ASP cc_start: 0.8539 (t70) cc_final: 0.8278 (t0) REVERT: D 100 TYR cc_start: 0.8214 (p90) cc_final: 0.7911 (p90) outliers start: 6 outliers final: 3 residues processed: 99 average time/residue: 0.0756 time to fit residues: 9.2044 Evaluate side-chains 89 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain D residue 61 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 HIS A 179 ASN B 226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.143883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104951 restraints weight = 5941.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108387 restraints weight = 3371.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110480 restraints weight = 2466.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111645 restraints weight = 2079.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111923 restraints weight = 1896.543| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4038 Z= 0.134 Angle : 0.533 5.573 5526 Z= 0.285 Chirality : 0.040 0.125 666 Planarity : 0.004 0.038 688 Dihedral : 4.181 17.676 577 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.09 % Allowed : 17.71 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.67 (0.35), residues: 527 helix: 0.19 (0.30), residues: 284 sheet: -2.24 (0.56), residues: 69 loop : -2.76 (0.41), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 176 TYR 0.013 0.001 TYR A 326 PHE 0.014 0.001 PHE A 187 TRP 0.009 0.001 TRP B 111 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 4037) covalent geometry : angle 0.53341 / 0.29 ( 5524) SS BOND : bond 0.00303 / 0.16 ( 1) SS BOND : angle 0.46790 / 0.26 ( 2) hydrogen bonds : bond 0.04082 / 2.97 ( 224) hydrogen bonds : angle 4.39542 / 3.18 ( 663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.7971 (mtp) cc_final: 0.7579 (mtt) REVERT: A 165 TRP cc_start: 0.4037 (m100) cc_final: 0.3824 (m100) REVERT: A 272 LYS cc_start: 0.8730 (tppp) cc_final: 0.8219 (tptt) REVERT: B 215 ASP cc_start: 0.8577 (t70) cc_final: 0.7815 (t0) outliers start: 15 outliers final: 8 residues processed: 98 average time/residue: 0.0775 time to fit residues: 9.2543 Evaluate side-chains 97 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain D residue 61 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.143439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107148 restraints weight = 5959.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107955 restraints weight = 3611.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.109590 restraints weight = 2894.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110015 restraints weight = 2299.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110338 restraints weight = 2246.672| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4038 Z= 0.148 Angle : 0.532 5.594 5526 Z= 0.281 Chirality : 0.041 0.125 666 Planarity : 0.004 0.034 688 Dihedral : 4.095 17.756 577 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.63 % Allowed : 19.62 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.36), residues: 527 helix: 0.56 (0.31), residues: 285 sheet: -2.15 (0.57), residues: 69 loop : -2.59 (0.42), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 176 TYR 0.013 0.001 TYR A 326 PHE 0.011 0.001 PHE A 297 TRP 0.008 0.001 TRP A 313 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 4037) covalent geometry : angle 0.53183 / 0.28 ( 5524) SS BOND : bond 0.00331 / 0.17 ( 1) SS BOND : angle 0.35796 / 0.20 ( 2) hydrogen bonds : bond 0.04176 / 3.05 ( 224) hydrogen bonds : angle 4.27624 / 3.10 ( 663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.164 Fit side-chains REVERT: A 165 TRP cc_start: 0.4029 (m100) cc_final: 0.3603 (m100) REVERT: A 177 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: A 179 ASN cc_start: 0.7896 (t0) cc_final: 0.7473 (t0) REVERT: A 272 LYS cc_start: 0.8733 (tppp) cc_final: 0.8195 (tptt) REVERT: B 215 ASP cc_start: 0.8568 (t70) cc_final: 0.7827 (t0) outliers start: 17 outliers final: 11 residues processed: 100 average time/residue: 0.0867 time to fit residues: 10.4458 Evaluate side-chains 100 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 39 optimal weight: 0.0010 chunk 37 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.145013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109124 restraints weight = 5924.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109565 restraints weight = 3685.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111089 restraints weight = 2950.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111396 restraints weight = 2366.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111837 restraints weight = 2274.562| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4038 Z= 0.115 Angle : 0.511 5.715 5526 Z= 0.269 Chirality : 0.040 0.157 666 Planarity : 0.004 0.033 688 Dihedral : 3.935 16.441 577 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.36 % Allowed : 20.16 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.37), residues: 527 helix: 0.87 (0.32), residues: 285 sheet: -1.94 (0.57), residues: 69 loop : -2.46 (0.43), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 176 TYR 0.013 0.001 TYR A 91 PHE 0.017 0.001 PHE A 187 TRP 0.008 0.001 TRP B 111 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 4037) covalent geometry : angle 0.51139 / 0.27 ( 5524) SS BOND : bond 0.00260 / 0.14 ( 1) SS BOND : angle 0.26521 / 0.15 ( 2) hydrogen bonds : bond 0.03889 / 2.84 ( 224) hydrogen bonds : angle 4.11021 / 2.97 ( 663) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.145 Fit side-chains REVERT: A 145 MET cc_start: 0.7601 (mmm) cc_final: 0.7167 (mtt) REVERT: A 165 TRP cc_start: 0.3913 (m100) cc_final: 0.3489 (m100) REVERT: A 179 ASN cc_start: 0.7707 (t0) cc_final: 0.7344 (t0) REVERT: A 272 LYS cc_start: 0.8691 (tppp) cc_final: 0.8222 (tptt) REVERT: B 215 ASP cc_start: 0.8467 (t70) cc_final: 0.7739 (t0) outliers start: 16 outliers final: 9 residues processed: 101 average time/residue: 0.0763 time to fit residues: 9.4581 Evaluate side-chains 98 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 100 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103927 restraints weight = 6036.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107402 restraints weight = 3458.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109278 restraints weight = 2548.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110578 restraints weight = 2175.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111054 restraints weight = 1985.511| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4038 Z= 0.141 Angle : 0.534 8.592 5526 Z= 0.279 Chirality : 0.040 0.124 666 Planarity : 0.003 0.032 688 Dihedral : 3.927 16.214 577 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.90 % Allowed : 21.53 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.37), residues: 527 helix: 0.92 (0.32), residues: 284 sheet: -1.85 (0.58), residues: 69 loop : -2.29 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 176 TYR 0.011 0.001 TYR A 326 PHE 0.009 0.001 PHE B 107 TRP 0.007 0.001 TRP A 102 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 4037) covalent geometry : angle 0.53376 / 0.28 ( 5524) SS BOND : bond 0.00330 / 0.17 ( 1) SS BOND : angle 0.40527 / 0.23 ( 2) hydrogen bonds : bond 0.04010 / 2.94 ( 224) hydrogen bonds : angle 4.14743 / 2.99 ( 663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.141 Fit side-chains REVERT: A 145 MET cc_start: 0.7617 (mmm) cc_final: 0.7194 (mtt) REVERT: A 165 TRP cc_start: 0.4005 (m100) cc_final: 0.3608 (m100) REVERT: A 179 ASN cc_start: 0.7894 (t0) cc_final: 0.7586 (t0) REVERT: A 272 LYS cc_start: 0.8706 (tppp) cc_final: 0.8229 (tptt) REVERT: B 215 ASP cc_start: 0.8500 (t70) cc_final: 0.7728 (t0) outliers start: 18 outliers final: 14 residues processed: 99 average time/residue: 0.0714 time to fit residues: 8.6496 Evaluate side-chains 102 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 100 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.0020 chunk 50 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.142573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102665 restraints weight = 6076.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106091 restraints weight = 3498.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107896 restraints weight = 2580.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109259 restraints weight = 2217.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109807 restraints weight = 2010.719| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4038 Z= 0.161 Angle : 0.555 9.041 5526 Z= 0.289 Chirality : 0.041 0.124 666 Planarity : 0.004 0.029 688 Dihedral : 3.987 16.995 577 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.09 % Allowed : 22.07 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.37), residues: 527 helix: 0.91 (0.32), residues: 285 sheet: -1.83 (0.58), residues: 69 loop : -2.11 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 176 TYR 0.013 0.001 TYR A 326 PHE 0.009 0.001 PHE B 107 TRP 0.008 0.001 TRP A 313 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 4037) covalent geometry : angle 0.55543 / 0.29 ( 5524) SS BOND : bond 0.00385 / 0.20 ( 1) SS BOND : angle 0.48114 / 0.27 ( 2) hydrogen bonds : bond 0.04201 / 3.08 ( 224) hydrogen bonds : angle 4.21843 / 3.04 ( 663) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.167 Fit side-chains REVERT: A 145 MET cc_start: 0.7674 (mmm) cc_final: 0.7339 (mtt) REVERT: A 165 TRP cc_start: 0.3978 (m100) cc_final: 0.3558 (m100) REVERT: A 179 ASN cc_start: 0.7947 (t0) cc_final: 0.7702 (t0) REVERT: A 272 LYS cc_start: 0.8708 (tppp) cc_final: 0.8224 (tptt) REVERT: B 215 ASP cc_start: 0.8579 (t70) cc_final: 0.7781 (t0) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.0814 time to fit residues: 9.1878 Evaluate side-chains 99 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.144781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.107821 restraints weight = 6042.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108029 restraints weight = 3713.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109853 restraints weight = 3009.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110034 restraints weight = 2423.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110436 restraints weight = 2360.622| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4038 Z= 0.119 Angle : 0.528 9.791 5526 Z= 0.273 Chirality : 0.040 0.127 666 Planarity : 0.003 0.032 688 Dihedral : 3.821 15.643 577 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.36 % Allowed : 20.98 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.38), residues: 527 helix: 1.14 (0.32), residues: 281 sheet: -1.64 (0.58), residues: 70 loop : -2.09 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 176 TYR 0.012 0.001 TYR A 91 PHE 0.007 0.001 PHE B 107 TRP 0.007 0.001 TRP B 111 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4037) covalent geometry : angle 0.52764 / 0.27 ( 5524) SS BOND : bond 0.00366 / 0.19 ( 1) SS BOND : angle 0.49849 / 0.28 ( 2) hydrogen bonds : bond 0.03827 / 2.81 ( 224) hydrogen bonds : angle 4.07510 / 2.94 ( 663) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.154 Fit side-chains REVERT: A 140 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: A 145 MET cc_start: 0.7595 (mmm) cc_final: 0.7281 (mtt) REVERT: A 165 TRP cc_start: 0.3776 (m100) cc_final: 0.3394 (m100) REVERT: A 181 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 269 LYS cc_start: 0.8553 (tptm) cc_final: 0.8143 (tppt) REVERT: A 272 LYS cc_start: 0.8679 (tppp) cc_final: 0.8225 (tptt) REVERT: B 215 ASP cc_start: 0.8474 (t70) cc_final: 0.7737 (t0) outliers start: 16 outliers final: 11 residues processed: 102 average time/residue: 0.0776 time to fit residues: 9.6766 Evaluate side-chains 102 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 30.0000 chunk 42 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 HIS B 71 GLN B 126 ASN B 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099336 restraints weight = 6188.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102565 restraints weight = 3606.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104344 restraints weight = 2692.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105621 restraints weight = 2315.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106127 restraints weight = 2109.092| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 4038 Z= 0.295 Angle : 0.669 8.776 5526 Z= 0.349 Chirality : 0.045 0.144 666 Planarity : 0.004 0.031 688 Dihedral : 4.357 18.995 577 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.09 % Allowed : 21.53 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.93 (0.36), residues: 527 helix: 0.64 (0.31), residues: 284 sheet: -1.97 (0.58), residues: 69 loop : -2.07 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 176 TYR 0.016 0.002 TYR A 326 PHE 0.013 0.002 PHE B 107 TRP 0.012 0.002 TRP A 313 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.29 ( 4037) covalent geometry : angle 0.66880 / 0.35 ( 5524) SS BOND : bond 0.00751 / 0.40 ( 1) SS BOND : angle 0.75547 / 0.44 ( 2) hydrogen bonds : bond 0.04976 / 3.65 ( 224) hydrogen bonds : angle 4.63289 / 3.35 ( 663) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.150 Fit side-chains REVERT: A 145 MET cc_start: 0.7743 (mmm) cc_final: 0.7421 (mtt) REVERT: A 165 TRP cc_start: 0.4395 (m100) cc_final: 0.3887 (m100) REVERT: A 269 LYS cc_start: 0.8575 (tptm) cc_final: 0.8221 (tppt) REVERT: A 272 LYS cc_start: 0.8806 (tppp) cc_final: 0.8264 (tptt) REVERT: B 215 ASP cc_start: 0.8667 (t70) cc_final: 0.8316 (t0) outliers start: 15 outliers final: 12 residues processed: 91 average time/residue: 0.0749 time to fit residues: 8.3876 Evaluate side-chains 92 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 HIS B 34 GLN B 71 GLN B 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107626 restraints weight = 5991.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107917 restraints weight = 3734.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109572 restraints weight = 2989.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109862 restraints weight = 2439.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110276 restraints weight = 2367.012| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4038 Z= 0.119 Angle : 0.546 10.202 5526 Z= 0.285 Chirality : 0.040 0.128 666 Planarity : 0.004 0.031 688 Dihedral : 3.969 18.416 577 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.00 % Allowed : 23.43 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.38), residues: 527 helix: 1.09 (0.32), residues: 280 sheet: -1.61 (0.60), residues: 69 loop : -2.01 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 176 TYR 0.015 0.001 TYR A 91 PHE 0.006 0.001 PHE B 56 TRP 0.009 0.001 TRP B 111 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 4037) covalent geometry : angle 0.54590 / 0.28 ( 5524) SS BOND : bond 0.00355 / 0.19 ( 1) SS BOND : angle 0.74000 / 0.41 ( 2) hydrogen bonds : bond 0.03919 / 2.88 ( 224) hydrogen bonds : angle 4.17565 / 3.01 ( 663) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.161 Fit side-chains REVERT: A 145 MET cc_start: 0.7596 (mmm) cc_final: 0.7284 (mtt) REVERT: A 165 TRP cc_start: 0.3872 (m100) cc_final: 0.3437 (m100) REVERT: A 181 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 269 LYS cc_start: 0.8558 (tptm) cc_final: 0.8137 (tppt) REVERT: A 272 LYS cc_start: 0.8701 (tppp) cc_final: 0.8186 (tptt) REVERT: B 215 ASP cc_start: 0.8473 (t70) cc_final: 0.7746 (t0) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.0817 time to fit residues: 9.3732 Evaluate side-chains 97 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain D residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101300 restraints weight = 6100.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104541 restraints weight = 3517.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106513 restraints weight = 2628.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107516 restraints weight = 2240.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107603 restraints weight = 2062.187| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4038 Z= 0.218 Angle : 0.619 9.396 5526 Z= 0.324 Chirality : 0.043 0.128 666 Planarity : 0.004 0.030 688 Dihedral : 4.143 17.430 577 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.27 % Allowed : 23.43 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.37), residues: 527 helix: 0.89 (0.31), residues: 285 sheet: -1.73 (0.59), residues: 69 loop : -1.98 (0.47), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 176 TYR 0.015 0.002 TYR A 91 PHE 0.010 0.001 PHE B 107 TRP 0.009 0.001 TRP A 102 HIS 0.004 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 ( 4037) covalent geometry : angle 0.61852 / 0.32 ( 5524) SS BOND : bond 0.00549 / 0.29 ( 1) SS BOND : angle 0.64739 / 0.37 ( 2) hydrogen bonds : bond 0.04485 / 3.30 ( 224) hydrogen bonds : angle 4.39411 / 3.18 ( 663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 952.06 seconds wall clock time: 17 minutes 4.45 seconds (1024.45 seconds total)