Starting phenix.real_space_refine on Fri Aug 22 14:21:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymh_33928/08_2025/7ymh_33928.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymh_33928/08_2025/7ymh_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_33928/08_2025/7ymh_33928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymh_33928/08_2025/7ymh_33928.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ymh_33928/08_2025/7ymh_33928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymh_33928/08_2025/7ymh_33928.map" } 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-2.0-5787/lib/python3.9/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: 1.49, per 1000 atoms: 0.38 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: 0.37 Conformation dependent library (CDL) restraints added in 246.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.14 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: 0.64 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: 1.23 - 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: 2063 15.48 - 30.95: 209 30.95 - 46.43: 49 46.43 - 61.90: 4 61.90 - 77.38: 4 Dihedral angle restraints: 2329 sinusoidal: 744 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 2326 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: 1.060 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 13.786 77.379 1300 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 aren 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 covalent geometry : bond 0.00420 ( 4037) covalent geometry : angle 0.77982 ( 5524) SS BOND : bond 0.00295 ( 1) SS BOND : angle 0.61919 ( 2) hydrogen bonds : bond 0.13040 ( 224) hydrogen bonds : angle 6.89403 ( 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 : 0.143 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: 0.8499 (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: 0.0890 time to fit residues: 12.2798 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 : 0.141 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108577 restraints weight = 6102.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109140 restraints weight = 3592.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110924 restraints weight = 2915.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111633 restraints weight = 2284.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111993 restraints weight = 2192.497| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1795 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= 0.136 Angle : 0.559 6.048 5526 Z= 0.303 Chirality : 0.040 0.127 666 Planarity : 0.005 0.042 688 Dihedral : 4.426 18.169 583 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.91 % Allowed : 15.53 % Favored : 82.56 % 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 aren 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 : -2.94 (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 197 TRP 0.009 0.001 TRP A 102 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4037) covalent geometry : angle 0.55863 ( 5524) SS BOND : bond 0.00263 ( 1) SS BOND : angle 0.36006 ( 2) hydrogen bonds : bond 0.04398 ( 224) hydrogen bonds : angle 4.72127 ( 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: 7 poor density : 96 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8043 (mtp) cc_final: 0.7637 (mtt) REVERT: A 165 TRP cc_start: 0.4216 (m100) cc_final: 0.3814 (m100) REVERT: A 272 LYS cc_start: 0.8727 (tppp) cc_final: 0.8222 (tptt) REVERT: B 215 ASP cc_start: 0.8538 (t70) cc_final: 0.8280 (t0) REVERT: D 100 TYR cc_start: 0.8215 (p90) cc_final: 0.7914 (p90) outliers start: 7 outliers final: 4 residues processed: 98 average time/residue: 0.0612 time to fit residues: 7.3168 Evaluate side-chains 89 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ASN 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: 0.6980 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.142984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103617 restraints weight = 5990.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107067 restraints weight = 3419.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109181 restraints weight = 2505.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110155 restraints weight = 2116.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110536 restraints weight = 1944.206| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2125 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= 0.149 Angle : 0.546 5.675 5526 Z= 0.292 Chirality : 0.041 0.127 666 Planarity : 0.004 0.037 688 Dihedral : 4.283 17.683 583 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.81 % Allowed : 18.26 % Favored : 77.93 % 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 aren not related in a simple way. whole: -1.79 (0.35), residues: 527 helix: 0.08 (0.30), residues: 282 sheet: -2.32 (0.56), residues: 69 loop : -2.72 (0.41), residues: 176 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 0.013 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 covalent geometry : bond 0.00339 ( 4037) covalent geometry : angle 0.54592 ( 5524) SS BOND : bond 0.00317 ( 1) SS BOND : angle 0.56027 ( 2) hydrogen bonds : bond 0.04207 ( 224) hydrogen bonds : angle 4.47710 ( 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 103 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.7992 (mtp) cc_final: 0.7557 (mtt) REVERT: A 165 TRP cc_start: 0.4159 (m100) cc_final: 0.3651 (m100) REVERT: A 179 ASN cc_start: 0.7508 (t0) cc_final: 0.7205 (t0) REVERT: A 272 LYS cc_start: 0.8744 (tppp) cc_final: 0.8240 (tptt) REVERT: B 215 ASP cc_start: 0.8591 (t70) cc_final: 0.7835 (t0) REVERT: D 100 TYR cc_start: 0.8136 (p90) cc_final: 0.7893 (p90) outliers start: 14 outliers final: 8 residues processed: 94 average time/residue: 0.0781 time to fit residues: 8.8879 Evaluate side-chains 94 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 205 CYS Chi-restraints excluded: chain A residue 262 LEU 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: 0.7980 chunk 49 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 179 ASN B 34 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 = 0.3798 r_free = 0.3798 target = 0.143685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108141 restraints weight = 5941.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108624 restraints weight = 3673.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110277 restraints weight = 2949.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110581 restraints weight = 2309.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110829 restraints weight = 2237.485| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2412 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= 0.132 Angle : 0.522 5.534 5526 Z= 0.275 Chirality : 0.040 0.124 666 Planarity : 0.004 0.031 688 Dihedral : 4.024 15.806 583 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.18 % Allowed : 19.07 % 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 aren not related in a simple way. whole: -1.23 (0.36), residues: 527 helix: 0.59 (0.31), residues: 285 sheet: -2.16 (0.56), residues: 69 loop : -2.61 (0.42), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 176 TYR 0.012 0.001 TYR A 326 PHE 0.009 0.001 PHE A 297 TRP 0.009 0.001 TRP B 111 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4037) covalent geometry : angle 0.52230 ( 5524) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.39248 ( 2) hydrogen bonds : bond 0.04046 ( 224) hydrogen bonds : angle 4.19694 ( 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 113 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.154 Fit side-chains REVERT: A 165 TRP cc_start: 0.4002 (m100) cc_final: 0.3499 (m100) REVERT: A 272 LYS cc_start: 0.8736 (tppp) cc_final: 0.8205 (tptt) REVERT: B 215 ASP cc_start: 0.8493 (t70) cc_final: 0.7793 (t0) REVERT: D 100 TYR cc_start: 0.8097 (p90) cc_final: 0.7891 (p90) outliers start: 19 outliers final: 12 residues processed: 100 average time/residue: 0.0787 time to fit residues: 9.4341 Evaluate side-chains 99 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 163 PHE 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: 7.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3789 r_free = 0.3789 target = 0.142943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.103535 restraints weight = 5957.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106954 restraints weight = 3425.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109001 restraints weight = 2530.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110059 restraints weight = 2148.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110782 restraints weight = 1968.259| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4038 Z= 0.150 Angle : 0.540 5.541 5526 Z= 0.284 Chirality : 0.041 0.171 666 Planarity : 0.004 0.028 688 Dihedral : 4.079 17.649 583 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.18 % Allowed : 19.35 % 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 aren not related in a simple way. whole: -1.01 (0.37), residues: 527 helix: 0.74 (0.32), residues: 285 sheet: -2.03 (0.58), residues: 69 loop : -2.44 (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 0.015 0.001 PHE A 187 TRP 0.009 0.001 TRP A 313 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4037) covalent geometry : angle 0.53961 ( 5524) SS BOND : bond 0.00376 ( 1) SS BOND : angle 0.44682 ( 2) hydrogen bonds : bond 0.04173 ( 224) hydrogen bonds : angle 4.22337 ( 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: 19 poor density : 94 time to evaluate : 0.087 Fit side-chains REVERT: A 145 MET cc_start: 0.7658 (mmm) cc_final: 0.7204 (mtt) REVERT: A 165 TRP cc_start: 0.4049 (m100) cc_final: 0.3615 (m100) REVERT: A 179 ASN cc_start: 0.8011 (t0) cc_final: 0.7626 (t0) REVERT: A 272 LYS cc_start: 0.8727 (tppp) cc_final: 0.8261 (tptt) REVERT: B 215 ASP cc_start: 0.8567 (t70) cc_final: 0.7792 (t0) REVERT: D 100 TYR cc_start: 0.8074 (p90) cc_final: 0.7839 (p90) outliers start: 19 outliers final: 12 residues processed: 100 average time/residue: 0.0788 time to fit residues: 9.3639 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 : 0.125 ------------------------------------------------------------------------------- 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 163 PHE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 317 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3778 r_free = 0.3778 target = 0.142383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102947 restraints weight = 6059.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106327 restraints weight = 3455.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108451 restraints weight = 2541.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109377 restraints weight = 2146.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110167 restraints weight = 1977.879| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 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 = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4038 Z= 0.159 Angle : 0.546 8.142 5526 Z= 0.287 Chirality : 0.041 0.165 666 Planarity : 0.004 0.028 688 Dihedral : 4.039 17.033 583 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.90 % Allowed : 20.44 % 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 aren not related in a simple way. whole: -0.83 (0.37), residues: 527 helix: 0.83 (0.32), residues: 285 sheet: -1.96 (0.58), residues: 69 loop : -2.26 (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 0.010 0.001 PHE B 107 TRP 0.009 0.001 TRP A 313 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 4037) covalent geometry : angle 0.54553 ( 5524) SS BOND : bond 0.00417 ( 1) SS BOND : angle 0.56073 ( 2) hydrogen bonds : bond 0.04216 ( 224) hydrogen bonds : angle 4.22304 ( 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 : 0.097 Fit side-chains REVERT: A 145 MET cc_start: 0.7638 (mmm) cc_final: 0.7228 (mtt) REVERT: A 165 TRP cc_start: 0.4062 (m100) cc_final: 0.3621 (m100) REVERT: A 179 ASN cc_start: 0.7941 (t0) cc_final: 0.7595 (t0) REVERT: A 272 LYS cc_start: 0.8731 (tppp) cc_final: 0.8249 (tptt) REVERT: B 215 ASP cc_start: 0.8579 (t70) cc_final: 0.7788 (t0) REVERT: D 100 TYR cc_start: 0.8087 (p90) cc_final: 0.7850 (p90) outliers start: 18 outliers final: 14 residues processed: 99 average time/residue: 0.0797 time to fit residues: 9.4415 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 : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU 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 162 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 292 MET Chi-restraints excluded: chain A residue 317 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 0.0060 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3806 r_free = 0.3806 target = 0.144868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105447 restraints weight = 6048.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108956 restraints weight = 3383.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110918 restraints weight = 2476.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112370 restraints weight = 2101.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112945 restraints weight = 1898.819| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4038 Z= 0.110 Angle : 0.518 9.617 5526 Z= 0.269 Chirality : 0.040 0.160 666 Planarity : 0.004 0.030 688 Dihedral : 3.814 16.611 583 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.81 % Allowed : 21.25 % Favored : 74.93 % 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 aren not related in a simple way. whole: -0.53 (0.38), residues: 527 helix: 1.11 (0.33), residues: 281 sheet: -1.69 (0.59), residues: 69 loop : -2.19 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 176 TYR 0.009 0.001 TYR A 326 PHE 0.007 0.001 PHE A 297 TRP 0.009 0.001 TRP B 111 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4037) covalent geometry : angle 0.51856 ( 5524) SS BOND : bond 0.00278 ( 1) SS BOND : angle 0.22348 ( 2) hydrogen bonds : bond 0.03776 ( 224) hydrogen bonds : angle 4.02514 ( 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 106 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.147 Fit side-chains REVERT: A 145 MET cc_start: 0.7579 (mmm) cc_final: 0.7251 (mtt) REVERT: A 165 TRP cc_start: 0.3946 (m100) cc_final: 0.3646 (m100) REVERT: A 179 ASN cc_start: 0.7846 (t0) cc_final: 0.7512 (t0) REVERT: A 272 LYS cc_start: 0.8680 (tppp) cc_final: 0.8203 (tptt) REVERT: B 215 ASP cc_start: 0.8459 (t70) cc_final: 0.7700 (t0) outliers start: 14 outliers final: 9 residues processed: 97 average time/residue: 0.0808 time to fit residues: 9.4475 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 : 0.145 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain B residue 226 ASN 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: 1.9990 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3798 r_free = 0.3798 target = 0.144067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104390 restraints weight = 6041.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107883 restraints weight = 3431.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110005 restraints weight = 2519.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110919 restraints weight = 2126.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111666 restraints weight = 1961.067| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 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 = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2833 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= 0.131 Angle : 0.545 9.489 5526 Z= 0.277 Chirality : 0.040 0.125 666 Planarity : 0.004 0.030 688 Dihedral : 3.840 15.604 583 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.81 % Allowed : 21.53 % 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 aren not related in a simple way. whole: -0.47 (0.37), residues: 527 helix: 1.05 (0.32), residues: 286 sheet: -1.63 (0.59), residues: 69 loop : -2.05 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 176 TYR 0.013 0.001 TYR D 99 PHE 0.008 0.001 PHE B 107 TRP 0.007 0.001 TRP A 313 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4037) covalent geometry : angle 0.54534 ( 5524) SS BOND : bond 0.00391 ( 1) SS BOND : angle 0.42773 ( 2) hydrogen bonds : bond 0.03925 ( 224) hydrogen bonds : angle 4.06948 ( 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 108 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.159 Fit side-chains REVERT: A 140 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: A 145 MET cc_start: 0.7621 (mmm) cc_final: 0.7272 (mtt) REVERT: A 165 TRP cc_start: 0.4062 (m100) cc_final: 0.3703 (m100) REVERT: A 179 ASN cc_start: 0.7892 (t0) cc_final: 0.7551 (t0) REVERT: A 181 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8070 (tm-30) REVERT: A 272 LYS cc_start: 0.8693 (tppp) cc_final: 0.8204 (tptt) REVERT: B 215 ASP cc_start: 0.8483 (t70) cc_final: 0.7716 (t0) outliers start: 14 outliers final: 12 residues processed: 100 average time/residue: 0.0739 time to fit residues: 8.9065 Evaluate side-chains 102 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.087 ------------------------------------------------------------------------------- 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 147 LEU Chi-restraints excluded: chain A residue 162 LEU 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 333 PHE Chi-restraints excluded: chain B residue 226 ASN 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: 2.9990 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 42 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3773 r_free = 0.3773 target = 0.141766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101784 restraints weight = 6144.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105190 restraints weight = 3519.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107232 restraints weight = 2600.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108342 restraints weight = 2210.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108687 restraints weight = 2026.103| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4038 Z= 0.178 Angle : 0.584 9.647 5526 Z= 0.298 Chirality : 0.042 0.128 666 Planarity : 0.004 0.030 688 Dihedral : 4.012 17.717 583 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.54 % Allowed : 22.34 % Favored : 74.11 % 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 aren not related in a simple way. whole: -0.56 (0.37), residues: 527 helix: 0.88 (0.31), residues: 291 sheet: -1.71 (0.59), residues: 70 loop : -1.96 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 176 TYR 0.015 0.001 TYR A 91 PHE 0.009 0.001 PHE B 107 TRP 0.011 0.001 TRP A 313 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 4037) covalent geometry : angle 0.58415 ( 5524) SS BOND : bond 0.00492 ( 1) SS BOND : angle 0.53904 ( 2) hydrogen bonds : bond 0.04285 ( 224) hydrogen bonds : angle 4.21592 ( 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 105 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.088 Fit side-chains REVERT: A 145 MET cc_start: 0.7673 (mmm) cc_final: 0.7342 (mtt) REVERT: A 165 TRP cc_start: 0.3918 (m100) cc_final: 0.3514 (m100) REVERT: A 179 ASN cc_start: 0.8052 (t0) cc_final: 0.7796 (t0) REVERT: A 272 LYS cc_start: 0.8706 (tppp) cc_final: 0.8219 (tptt) REVERT: B 215 ASP cc_start: 0.8588 (t70) cc_final: 0.7788 (t0) outliers start: 13 outliers final: 13 residues processed: 96 average time/residue: 0.0721 time to fit residues: 8.3808 Evaluate side-chains 102 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 162 LEU 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 B residue 226 ASN Chi-restraints excluded: chain D residue 61 SER 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: 0.7980 chunk 35 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS B 71 GLN B 226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.145804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109377 restraints weight = 5956.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109499 restraints weight = 3695.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111293 restraints weight = 2983.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111831 restraints weight = 2380.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112164 restraints weight = 2314.637| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4038 Z= 0.105 Angle : 0.538 10.358 5526 Z= 0.271 Chirality : 0.039 0.132 666 Planarity : 0.004 0.029 688 Dihedral : 3.794 15.381 583 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.54 % Allowed : 22.34 % Favored : 74.11 % 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 aren not related in a simple way. whole: -0.25 (0.38), residues: 527 helix: 1.17 (0.32), residues: 288 sheet: -1.52 (0.59), residues: 69 loop : -1.87 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 176 TYR 0.016 0.001 TYR A 91 PHE 0.009 0.001 PHE A 94 TRP 0.010 0.001 TRP B 111 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 4037) covalent geometry : angle 0.53815 ( 5524) SS BOND : bond 0.00305 ( 1) SS BOND : angle 0.44854 ( 2) hydrogen bonds : bond 0.03732 ( 224) hydrogen bonds : angle 3.96752 ( 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 109 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.139 Fit side-chains REVERT: A 140 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7483 (mp10) REVERT: A 145 MET cc_start: 0.7537 (mmm) cc_final: 0.7254 (mtt) REVERT: A 165 TRP cc_start: 0.3821 (m100) cc_final: 0.3490 (m100) REVERT: A 181 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 272 LYS cc_start: 0.8663 (tppp) cc_final: 0.8187 (tptt) REVERT: B 35 MET cc_start: 0.7817 (pmm) cc_final: 0.7512 (pmm) REVERT: B 215 ASP cc_start: 0.8441 (t70) cc_final: 0.7799 (t0) outliers start: 13 outliers final: 10 residues processed: 104 average time/residue: 0.0679 time to fit residues: 8.5549 Evaluate side-chains 103 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 162 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.0010 chunk 28 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.144548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107535 restraints weight = 6037.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108119 restraints weight = 3731.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109772 restraints weight = 2985.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110241 restraints weight = 2409.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110562 restraints weight = 2350.517| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.109 | | 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) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4038 Z= 0.119 Angle : 0.544 9.919 5526 Z= 0.273 Chirality : 0.040 0.127 666 Planarity : 0.004 0.029 688 Dihedral : 3.732 15.373 583 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.27 % Allowed : 22.89 % 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 aren not related in a simple way. whole: -0.24 (0.38), residues: 527 helix: 1.19 (0.32), residues: 286 sheet: -1.51 (0.59), residues: 70 loop : -1.87 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 176 TYR 0.015 0.001 TYR A 91 PHE 0.007 0.001 PHE A 193 TRP 0.008 0.001 TRP B 111 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4037) covalent geometry : angle 0.54377 ( 5524) SS BOND : bond 0.00347 ( 1) SS BOND : angle 0.44043 ( 2) hydrogen bonds : bond 0.03816 ( 224) hydrogen bonds : angle 3.99845 ( 663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 882.44 seconds wall clock time: 15 minutes 59.94 seconds (959.94 seconds total)