Starting phenix.real_space_refine on Wed Jul 1 23:42:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8de7_27386/07_2026/8de7_27386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de7_27386/07_2026/8de7_27386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8de7_27386/07_2026/8de7_27386.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8de7_27386/07_2026/8de7_27386.cif" model { file = "/net/cci-nas-00/data/ceres_data/8de7_27386/07_2026/8de7_27386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de7_27386/07_2026/8de7_27386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8de7_27386/07_2026/8de7_27386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de7_27386/07_2026/8de7_27386.map" } resolution = 3.27 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= 0.002 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: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 16 5.16 5 C 2789 2.51 5 N 637 2.21 5 O 723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 4168 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2067 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 7, 'TRANS': 255} Chain: "A" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2063 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 255} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.25, per 1000 atoms: 0.30 Number of scatterers: 4168 At special positions: 0 Unit cell: (80.7, 79.624, 94.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 16 16.00 O 723 8.00 N 637 7.00 C 2789 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS A 93 " 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: 0.23 Conformation dependent library (CDL) restraints added in 124.5 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 956 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'B' and resid 43 through 91 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 95 through 113 Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 152 through 194 removed outlier: 3.738A pdb=" N ILE B 157 " --> pdb=" O GLU B 153 " (cutoff:3.500A) Proline residue: B 168 - end of helix removed outlier: 4.078A pdb=" N LYS B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 223 Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 237 through 251 removed outlier: 3.641A pdb=" N ILE B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 302 Processing helix chain 'A' and resid 43 through 91 Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 95 through 113 Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 152 through 197 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 202 through 223 removed outlier: 3.888A pdb=" N ARG A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 270 through 301 removed outlier: 3.982A pdb=" N ALA A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 1002 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: 0.63 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1199 1.34 - 1.46: 807 1.46 - 1.58: 2240 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 4272 Sorted by residual: bond pdb=" C1B LMT B 401 " pdb=" O5B LMT B 401 " ideal model delta sigma weight residual 1.393 1.502 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C1' LMT B 401 " pdb=" O5' LMT B 401 " ideal model delta sigma weight residual 1.408 1.503 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C5' LMT B 401 " pdb=" O5' LMT B 401 " ideal model delta sigma weight residual 1.411 1.473 -0.062 2.00e-02 2.50e+03 9.76e+00 bond pdb=" C5B LMT B 401 " pdb=" O5B LMT B 401 " ideal model delta sigma weight residual 1.422 1.479 -0.057 2.00e-02 2.50e+03 8.18e+00 bond pdb=" C3B LMT B 401 " pdb=" O3B LMT B 401 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.89e+00 ... (remaining 4267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 5578 2.51 - 5.02: 186 5.02 - 7.52: 34 7.52 - 10.03: 3 10.03 - 12.54: 2 Bond angle restraints: 5803 Sorted by residual: angle pdb=" N VAL A 197 " pdb=" CA VAL A 197 " pdb=" C VAL A 197 " ideal model delta sigma weight residual 110.62 114.52 -3.90 1.02e+00 9.61e-01 1.46e+01 angle pdb=" N GLY A 166 " pdb=" CA GLY A 166 " pdb=" C GLY A 166 " ideal model delta sigma weight residual 112.77 117.60 -4.83 1.28e+00 6.10e-01 1.42e+01 angle pdb=" CA LEU A 267 " pdb=" CB LEU A 267 " pdb=" CG LEU A 267 " ideal model delta sigma weight residual 116.30 128.84 -12.54 3.50e+00 8.16e-02 1.28e+01 angle pdb=" CA LEU B 169 " pdb=" CB LEU B 169 " pdb=" CG LEU B 169 " ideal model delta sigma weight residual 116.30 128.68 -12.38 3.50e+00 8.16e-02 1.25e+01 angle pdb=" CA THR B 152 " pdb=" CB THR B 152 " pdb=" CG2 THR B 152 " ideal model delta sigma weight residual 110.50 116.33 -5.83 1.70e+00 3.46e-01 1.18e+01 ... (remaining 5798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2170 17.96 - 35.91: 205 35.91 - 53.87: 39 53.87 - 71.83: 5 71.83 - 89.78: 9 Dihedral angle restraints: 2428 sinusoidal: 932 harmonic: 1496 Sorted by residual: dihedral pdb=" CB CYS B 93 " pdb=" SG CYS B 93 " pdb=" SG CYS A 93 " pdb=" CB CYS A 93 " ideal model delta sinusoidal sigma weight residual -86.00 -165.74 79.74 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB GLU A 83 " pdb=" CG GLU A 83 " pdb=" CD GLU A 83 " pdb=" OE1 GLU A 83 " ideal model delta sinusoidal sigma weight residual 0.00 89.78 -89.78 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" C ILE A 167 " pdb=" N ILE A 167 " pdb=" CA ILE A 167 " pdb=" CB ILE A 167 " ideal model delta harmonic sigma weight residual -122.00 -129.91 7.91 0 2.50e+00 1.60e-01 1.00e+01 ... (remaining 2425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 499 0.052 - 0.103: 125 0.103 - 0.155: 49 0.155 - 0.206: 7 0.206 - 0.258: 8 Chirality restraints: 688 Sorted by residual: chirality pdb=" CB THR A 138 " pdb=" CA THR A 138 " pdb=" OG1 THR A 138 " pdb=" CG2 THR A 138 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA GLN B 70 " pdb=" N GLN B 70 " pdb=" C GLN B 70 " pdb=" CB GLN B 70 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU B 169 " pdb=" CB LEU B 169 " pdb=" CD1 LEU B 169 " pdb=" CD2 LEU B 169 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 685 not shown) Planarity restraints: 692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 149 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO B 150 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 115 " 0.046 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO A 116 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 149 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A 150 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.037 5.00e-02 4.00e+02 ... (remaining 689 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.87: 1466 2.87 - 3.44: 5212 3.44 - 4.01: 7477 4.01 - 4.57: 10627 4.57 - 5.14: 14643 Nonbonded interactions: 39425 Sorted by model distance: nonbonded pdb=" OG SER B 121 " pdb=" OG SER B 124 " model vdw 2.304 3.040 nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR A 266 " model vdw 2.349 3.040 nonbonded pdb=" NZ LYS B 84 " pdb=" O PRO A 116 " model vdw 2.351 3.120 nonbonded pdb=" O ALA A 287 " pdb=" OG SER A 290 " model vdw 2.358 3.040 nonbonded pdb=" O ARG A 111 " pdb=" NE2 HIS A 151 " model vdw 2.380 3.120 ... (remaining 39420 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 41 through 301) selection = (chain 'B' and resid 41 through 301) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 6.050 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.000 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.006 0.109 4273 Z= 0.302 Angle : 1.055 12.541 5805 Z= 0.578 Chirality : 0.058 0.258 688 Planarity : 0.008 0.069 692 Dihedral : 14.999 89.782 1469 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.90 % Allowed : 0.22 % Favored : 98.88 % 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: 4.08 (0.33), residues: 522 helix: 3.44 (0.22), residues: 402 sheet: None (None), residues: 0 loop : -0.10 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 207 TYR 0.017 0.003 TYR B 266 PHE 0.023 0.003 PHE A 285 TRP 0.033 0.003 TRP A 199 HIS 0.006 0.002 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.30 ( 4272) covalent geometry : angle 1.05109 / 0.58 ( 5803) SS BOND : bond 0.00150 / 0.08 ( 1) SS BOND : angle 5.25403 / 3.01 ( 2) hydrogen bonds : bond 0.08583 / 5.42 ( 334) hydrogen bonds : angle 4.65791 / 3.46 ( 1002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 251 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.9398 (tp) cc_final: 0.9120 (tp) REVERT: B 82 GLN cc_start: 0.9328 (mm110) cc_final: 0.9022 (mm-40) REVERT: B 96 THR cc_start: 0.9353 (t) cc_final: 0.8967 (p) REVERT: B 99 LEU cc_start: 0.9722 (tp) cc_final: 0.9386 (tp) REVERT: B 101 ASP cc_start: 0.9448 (t0) cc_final: 0.9203 (m-30) REVERT: B 104 LYS cc_start: 0.9481 (ttmm) cc_final: 0.9228 (mtmm) REVERT: B 215 ILE cc_start: 0.9649 (mt) cc_final: 0.9306 (mt) REVERT: B 231 GLN cc_start: 0.8610 (tt0) cc_final: 0.8370 (tt0) REVERT: A 48 LEU cc_start: 0.9520 (tp) cc_final: 0.9291 (tp) REVERT: A 52 LEU cc_start: 0.9366 (mt) cc_final: 0.9164 (mt) REVERT: A 56 LEU cc_start: 0.9303 (tp) cc_final: 0.9048 (tp) REVERT: A 66 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8385 (ttmm) REVERT: A 77 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8857 (mmmm) REVERT: A 82 GLN cc_start: 0.9406 (tp40) cc_final: 0.9141 (mm-40) REVERT: A 95 GLN cc_start: 0.9193 (mm110) cc_final: 0.8634 (mm110) REVERT: A 101 ASP cc_start: 0.9146 (m-30) cc_final: 0.7925 (m-30) REVERT: A 104 LYS cc_start: 0.9540 (ttpp) cc_final: 0.9311 (mtmm) REVERT: A 105 GLN cc_start: 0.9524 (mm110) cc_final: 0.9259 (mm-40) REVERT: A 191 LYS cc_start: 0.8595 (mttp) cc_final: 0.8100 (ttmm) REVERT: A 196 PHE cc_start: 0.9018 (t80) cc_final: 0.8692 (t80) REVERT: A 216 LEU cc_start: 0.9372 (mp) cc_final: 0.9109 (mp) REVERT: A 225 LEU cc_start: 0.9268 (tp) cc_final: 0.9038 (tp) REVERT: A 269 TYR cc_start: 0.8095 (m-80) cc_final: 0.7592 (m-80) outliers start: 4 outliers final: 1 residues processed: 253 average time/residue: 0.0650 time to fit residues: 20.7702 Evaluate side-chains 213 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN A 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.153654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106734 restraints weight = 7190.142| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.98 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4273 Z= 0.183 Angle : 0.761 12.902 5805 Z= 0.379 Chirality : 0.045 0.161 688 Planarity : 0.005 0.047 692 Dihedral : 6.047 55.117 562 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.82 % Allowed : 20.00 % Favored : 76.18 % 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: 3.72 (0.35), residues: 522 helix: 3.20 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -0.52 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 79 TYR 0.014 0.002 TYR B 162 PHE 0.019 0.002 PHE B 51 TRP 0.014 0.002 TRP A 277 HIS 0.005 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 4272) covalent geometry : angle 0.76017 / 0.38 ( 5803) SS BOND : bond 0.00270 / 0.14 ( 1) SS BOND : angle 1.87827 / 1.08 ( 2) hydrogen bonds : bond 0.04617 / 2.97 ( 334) hydrogen bonds : angle 4.19762 / 3.10 ( 1002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9497 (mm110) cc_final: 0.9192 (mm-40) REVERT: B 98 GLU cc_start: 0.9493 (mp0) cc_final: 0.9263 (mp0) REVERT: B 101 ASP cc_start: 0.9615 (t0) cc_final: 0.9264 (m-30) REVERT: B 104 LYS cc_start: 0.9448 (ttmm) cc_final: 0.9178 (mtmm) REVERT: B 231 GLN cc_start: 0.9119 (tt0) cc_final: 0.8488 (tt0) REVERT: B 269 TYR cc_start: 0.8188 (m-80) cc_final: 0.7927 (m-80) REVERT: A 42 MET cc_start: 0.8435 (mmm) cc_final: 0.8205 (mmm) REVERT: A 48 LEU cc_start: 0.9485 (tp) cc_final: 0.9244 (tp) REVERT: A 52 LEU cc_start: 0.9534 (mt) cc_final: 0.9309 (mt) REVERT: A 56 LEU cc_start: 0.9623 (tp) cc_final: 0.9399 (tp) REVERT: A 101 ASP cc_start: 0.8666 (m-30) cc_final: 0.8390 (m-30) REVERT: A 104 LYS cc_start: 0.9598 (ttpp) cc_final: 0.9262 (mtmm) REVERT: A 216 LEU cc_start: 0.9459 (mp) cc_final: 0.9236 (mp) REVERT: A 269 TYR cc_start: 0.8394 (m-80) cc_final: 0.7936 (m-80) outliers start: 17 outliers final: 8 residues processed: 223 average time/residue: 0.0553 time to fit residues: 15.9909 Evaluate side-chains 210 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.152813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105506 restraints weight = 7212.284| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 4.00 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4273 Z= 0.171 Angle : 0.735 10.372 5805 Z= 0.369 Chirality : 0.043 0.173 688 Planarity : 0.005 0.058 692 Dihedral : 5.671 52.300 561 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.70 % Allowed : 22.92 % Favored : 74.38 % 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: 3.31 (0.35), residues: 522 helix: 2.97 (0.23), residues: 407 sheet: None (None), residues: 0 loop : -0.90 (0.53), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 79 TYR 0.020 0.002 TYR A 266 PHE 0.019 0.001 PHE A 158 TRP 0.015 0.001 TRP A 277 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 4272) covalent geometry : angle 0.73443 / 0.37 ( 5803) SS BOND : bond 0.00113 / 0.06 ( 1) SS BOND : angle 1.59430 / 0.93 ( 2) hydrogen bonds : bond 0.04205 / 2.69 ( 334) hydrogen bonds : angle 4.09530 / 3.04 ( 1002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9496 (mm110) cc_final: 0.9129 (mm-40) REVERT: B 101 ASP cc_start: 0.9641 (t0) cc_final: 0.9311 (m-30) REVERT: B 104 LYS cc_start: 0.9437 (ttmm) cc_final: 0.9174 (mtmm) REVERT: B 195 MET cc_start: 0.4744 (mmm) cc_final: 0.4498 (mmm) REVERT: B 231 GLN cc_start: 0.9004 (tt0) cc_final: 0.8273 (tt0) REVERT: B 269 TYR cc_start: 0.8164 (m-80) cc_final: 0.7942 (m-80) REVERT: B 289 LEU cc_start: 0.8739 (mp) cc_final: 0.8526 (mp) REVERT: A 42 MET cc_start: 0.8506 (mmm) cc_final: 0.8202 (mmm) REVERT: A 48 LEU cc_start: 0.9483 (tp) cc_final: 0.9258 (tp) REVERT: A 52 LEU cc_start: 0.9553 (mt) cc_final: 0.9333 (mt) REVERT: A 56 LEU cc_start: 0.9617 (tp) cc_final: 0.9405 (tp) REVERT: A 98 GLU cc_start: 0.9026 (pt0) cc_final: 0.8789 (pt0) REVERT: A 99 LEU cc_start: 0.9426 (pp) cc_final: 0.8902 (pp) REVERT: A 104 LYS cc_start: 0.9577 (ttpp) cc_final: 0.9256 (mtmm) REVERT: A 122 GLN cc_start: 0.8737 (pm20) cc_final: 0.8448 (pm20) REVERT: A 228 LEU cc_start: 0.9546 (mm) cc_final: 0.9340 (mm) REVERT: A 269 TYR cc_start: 0.8420 (m-80) cc_final: 0.7985 (m-80) REVERT: A 270 TYR cc_start: 0.8322 (t80) cc_final: 0.8106 (t80) outliers start: 12 outliers final: 7 residues processed: 212 average time/residue: 0.0571 time to fit residues: 15.8917 Evaluate side-chains 208 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 201 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 29 optimal weight: 0.0050 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN A 180 GLN A 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.151831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102218 restraints weight = 7215.033| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 4.26 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4273 Z= 0.158 Angle : 0.737 10.393 5805 Z= 0.362 Chirality : 0.044 0.272 688 Planarity : 0.005 0.065 692 Dihedral : 5.072 43.196 561 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.60 % Allowed : 27.19 % Favored : 69.21 % 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: 3.08 (0.36), residues: 522 helix: 2.82 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.13 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 79 TYR 0.012 0.002 TYR A 266 PHE 0.037 0.002 PHE A 196 TRP 0.010 0.001 TRP B 44 HIS 0.005 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 4272) covalent geometry : angle 0.73647 / 0.36 ( 5803) SS BOND : bond 0.00025 / 0.01 ( 1) SS BOND : angle 1.39755 / 0.82 ( 2) hydrogen bonds : bond 0.04042 / 2.60 ( 334) hydrogen bonds : angle 4.12986 / 3.06 ( 1002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 TRP cc_start: 0.7814 (t60) cc_final: 0.7580 (t60) REVERT: B 48 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9174 (mp) REVERT: B 82 GLN cc_start: 0.9513 (mm110) cc_final: 0.9131 (mm-40) REVERT: B 95 GLN cc_start: 0.9176 (mp10) cc_final: 0.8876 (mp10) REVERT: B 101 ASP cc_start: 0.9641 (t0) cc_final: 0.9306 (m-30) REVERT: B 104 LYS cc_start: 0.9452 (ttmm) cc_final: 0.9197 (mtmm) REVERT: B 231 GLN cc_start: 0.8992 (tt0) cc_final: 0.8272 (tt0) REVERT: B 240 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7913 (pt0) REVERT: B 270 TYR cc_start: 0.8409 (t80) cc_final: 0.8075 (t80) REVERT: B 289 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8523 (mp) REVERT: A 42 MET cc_start: 0.8419 (mmm) cc_final: 0.8127 (mmm) REVERT: A 48 LEU cc_start: 0.9484 (tp) cc_final: 0.9241 (tp) REVERT: A 51 PHE cc_start: 0.9165 (t80) cc_final: 0.8936 (t80) REVERT: A 52 LEU cc_start: 0.9546 (mt) cc_final: 0.9339 (mt) REVERT: A 56 LEU cc_start: 0.9611 (tp) cc_final: 0.9411 (tp) REVERT: A 98 GLU cc_start: 0.9081 (pt0) cc_final: 0.8830 (pt0) REVERT: A 99 LEU cc_start: 0.9432 (pp) cc_final: 0.8841 (pp) REVERT: A 100 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9030 (mm-30) REVERT: A 104 LYS cc_start: 0.9539 (ttpp) cc_final: 0.9281 (mtmm) REVERT: A 122 GLN cc_start: 0.8772 (pm20) cc_final: 0.8409 (pm20) REVERT: A 263 GLU cc_start: 0.8467 (pp20) cc_final: 0.8230 (pp20) REVERT: A 268 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7551 (p0) REVERT: A 269 TYR cc_start: 0.8462 (m-80) cc_final: 0.7893 (m-80) REVERT: A 270 TYR cc_start: 0.8280 (t80) cc_final: 0.8018 (t80) outliers start: 16 outliers final: 9 residues processed: 214 average time/residue: 0.0570 time to fit residues: 15.9853 Evaluate side-chains 216 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 204 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 0.0980 chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.153747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103766 restraints weight = 7237.765| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 4.35 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4273 Z= 0.155 Angle : 0.738 8.898 5805 Z= 0.363 Chirality : 0.043 0.258 688 Planarity : 0.005 0.061 692 Dihedral : 4.781 40.115 561 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.49 % Allowed : 28.99 % Favored : 66.52 % 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: 2.81 (0.36), residues: 522 helix: 2.61 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.15 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 297 TYR 0.009 0.002 TYR A 266 PHE 0.016 0.001 PHE A 51 TRP 0.013 0.001 TRP B 44 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 4272) covalent geometry : angle 0.73790 / 0.36 ( 5803) SS BOND : bond 0.00015 / 0.01 ( 1) SS BOND : angle 1.32147 / 0.77 ( 2) hydrogen bonds : bond 0.03939 / 2.52 ( 334) hydrogen bonds : angle 4.20605 / 3.09 ( 1002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLN cc_start: 0.9519 (mm110) cc_final: 0.9162 (mm-40) REVERT: B 95 GLN cc_start: 0.9153 (mp10) cc_final: 0.8865 (mp10) REVERT: B 101 ASP cc_start: 0.9642 (t0) cc_final: 0.9255 (m-30) REVERT: B 103 VAL cc_start: 0.9340 (t) cc_final: 0.9124 (m) REVERT: B 104 LYS cc_start: 0.9450 (ttmm) cc_final: 0.9156 (mtmm) REVERT: B 195 MET cc_start: 0.4598 (mmm) cc_final: 0.3878 (ptp) REVERT: B 231 GLN cc_start: 0.8970 (tt0) cc_final: 0.8241 (tt0) REVERT: B 240 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7900 (pt0) REVERT: B 270 TYR cc_start: 0.8383 (t80) cc_final: 0.8110 (t80) REVERT: B 289 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8596 (mp) REVERT: A 42 MET cc_start: 0.8489 (mmm) cc_final: 0.8255 (mmm) REVERT: A 48 LEU cc_start: 0.9494 (tp) cc_final: 0.9237 (tp) REVERT: A 51 PHE cc_start: 0.9162 (t80) cc_final: 0.8914 (t80) REVERT: A 52 LEU cc_start: 0.9544 (mt) cc_final: 0.9336 (mt) REVERT: A 56 LEU cc_start: 0.9607 (tp) cc_final: 0.9401 (tp) REVERT: A 104 LYS cc_start: 0.9531 (ttpp) cc_final: 0.9263 (ptpp) REVERT: A 122 GLN cc_start: 0.8836 (pm20) cc_final: 0.8417 (pm20) REVERT: A 151 HIS cc_start: 0.8488 (m90) cc_final: 0.7952 (m-70) REVERT: A 207 ARG cc_start: 0.8644 (tmt170) cc_final: 0.8318 (tpt90) REVERT: A 240 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8188 (mt-10) REVERT: A 263 GLU cc_start: 0.8572 (pp20) cc_final: 0.8343 (pp20) REVERT: A 268 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7517 (p0) REVERT: A 269 TYR cc_start: 0.8428 (m-80) cc_final: 0.7857 (m-80) outliers start: 20 outliers final: 12 residues processed: 212 average time/residue: 0.0566 time to fit residues: 15.7309 Evaluate side-chains 216 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 47 optimal weight: 0.2980 chunk 48 optimal weight: 0.1980 chunk 5 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.153798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103486 restraints weight = 7365.193| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 4.34 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4273 Z= 0.157 Angle : 0.743 14.083 5805 Z= 0.364 Chirality : 0.042 0.166 688 Planarity : 0.005 0.062 692 Dihedral : 4.614 40.367 561 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.49 % Allowed : 32.13 % Favored : 63.37 % 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: 2.68 (0.36), residues: 522 helix: 2.51 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.16 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 79 TYR 0.012 0.002 TYR B 284 PHE 0.021 0.001 PHE B 51 TRP 0.021 0.001 TRP A 277 HIS 0.003 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 4272) covalent geometry : angle 0.74308 / 0.36 ( 5803) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 1.00905 / 0.59 ( 2) hydrogen bonds : bond 0.03923 / 2.50 ( 334) hydrogen bonds : angle 4.24092 / 3.11 ( 1002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 GLN cc_start: 0.9126 (mp10) cc_final: 0.8889 (mp10) REVERT: B 101 ASP cc_start: 0.9652 (t0) cc_final: 0.9254 (m-30) REVERT: B 104 LYS cc_start: 0.9440 (ttmm) cc_final: 0.9165 (mtmm) REVERT: B 231 GLN cc_start: 0.8938 (tt0) cc_final: 0.8188 (tt0) REVERT: B 240 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7898 (pt0) REVERT: B 270 TYR cc_start: 0.8373 (t80) cc_final: 0.8092 (t80) REVERT: B 289 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 48 LEU cc_start: 0.9483 (tp) cc_final: 0.9221 (tp) REVERT: A 51 PHE cc_start: 0.9129 (t80) cc_final: 0.8886 (t80) REVERT: A 52 LEU cc_start: 0.9528 (mt) cc_final: 0.9316 (mt) REVERT: A 56 LEU cc_start: 0.9581 (tp) cc_final: 0.9374 (tp) REVERT: A 79 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.9134 (ptm-80) REVERT: A 98 GLU cc_start: 0.9513 (mp0) cc_final: 0.9189 (pm20) REVERT: A 100 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9088 (mm-30) REVERT: A 104 LYS cc_start: 0.9512 (ttpp) cc_final: 0.9253 (mtmm) REVERT: A 122 GLN cc_start: 0.8924 (pm20) cc_final: 0.8539 (pm20) REVERT: A 151 HIS cc_start: 0.8553 (m90) cc_final: 0.8029 (m-70) REVERT: A 240 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8186 (mt-10) REVERT: A 263 GLU cc_start: 0.8646 (pp20) cc_final: 0.8387 (pp20) REVERT: A 268 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7482 (p0) REVERT: A 269 TYR cc_start: 0.8437 (m-80) cc_final: 0.7757 (m-80) outliers start: 20 outliers final: 12 residues processed: 214 average time/residue: 0.0592 time to fit residues: 16.5586 Evaluate side-chains 218 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.151366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099225 restraints weight = 7375.915| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.25 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 4273 Z= 0.202 Angle : 0.812 12.281 5805 Z= 0.402 Chirality : 0.044 0.198 688 Planarity : 0.006 0.067 692 Dihedral : 4.698 39.741 561 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.72 % Allowed : 34.38 % Favored : 60.90 % 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: 2.46 (0.35), residues: 522 helix: 2.36 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.24 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 207 TYR 0.010 0.002 TYR B 269 PHE 0.019 0.002 PHE B 158 TRP 0.011 0.002 TRP A 236 HIS 0.003 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.20 ( 4272) covalent geometry : angle 0.81162 / 0.40 ( 5803) SS BOND : bond 0.00986 / 0.52 ( 1) SS BOND : angle 0.52708 / 0.30 ( 2) hydrogen bonds : bond 0.04000 / 2.57 ( 334) hydrogen bonds : angle 4.34662 / 3.19 ( 1002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 GLN cc_start: 0.9203 (mp10) cc_final: 0.8985 (mp10) REVERT: B 101 ASP cc_start: 0.9650 (t0) cc_final: 0.9299 (m-30) REVERT: B 104 LYS cc_start: 0.9463 (ttmm) cc_final: 0.9207 (mtmm) REVERT: B 231 GLN cc_start: 0.8933 (tt0) cc_final: 0.8215 (tt0) REVERT: B 270 TYR cc_start: 0.8374 (t80) cc_final: 0.8065 (t80) REVERT: A 42 MET cc_start: 0.8401 (mmm) cc_final: 0.8106 (mmp) REVERT: A 48 LEU cc_start: 0.9488 (tp) cc_final: 0.9226 (tp) REVERT: A 51 PHE cc_start: 0.9120 (t80) cc_final: 0.8906 (t80) REVERT: A 52 LEU cc_start: 0.9549 (mt) cc_final: 0.9324 (mt) REVERT: A 79 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.9128 (ptm160) REVERT: A 95 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8756 (mm-40) REVERT: A 98 GLU cc_start: 0.9498 (mp0) cc_final: 0.9188 (pm20) REVERT: A 122 GLN cc_start: 0.8972 (pm20) cc_final: 0.8603 (pm20) REVERT: A 151 HIS cc_start: 0.8622 (m90) cc_final: 0.8165 (m170) REVERT: A 240 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 263 GLU cc_start: 0.8705 (pp20) cc_final: 0.8464 (pp20) REVERT: A 268 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7528 (p0) REVERT: A 269 TYR cc_start: 0.8477 (m-80) cc_final: 0.7750 (m-80) outliers start: 21 outliers final: 15 residues processed: 206 average time/residue: 0.0549 time to fit residues: 14.8340 Evaluate side-chains 216 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 49 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.152824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.101839 restraints weight = 7380.709| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 4.30 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4273 Z= 0.161 Angle : 0.832 12.797 5805 Z= 0.401 Chirality : 0.044 0.306 688 Planarity : 0.005 0.061 692 Dihedral : 4.593 40.144 561 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.82 % Allowed : 35.28 % Favored : 60.90 % 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: 2.41 (0.36), residues: 522 helix: 2.33 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -1.24 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 79 TYR 0.011 0.002 TYR B 284 PHE 0.020 0.001 PHE B 51 TRP 0.011 0.001 TRP A 277 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 4272) covalent geometry : angle 0.83184 / 0.40 ( 5803) SS BOND : bond 0.00502 / 0.26 ( 1) SS BOND : angle 0.14342 / 0.08 ( 2) hydrogen bonds : bond 0.03926 / 2.49 ( 334) hydrogen bonds : angle 4.38282 / 3.21 ( 1002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 LYS cc_start: 0.9460 (ttmm) cc_final: 0.9173 (mtmm) REVERT: B 231 GLN cc_start: 0.8869 (tt0) cc_final: 0.8111 (tt0) REVERT: B 240 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7830 (pt0) REVERT: A 48 LEU cc_start: 0.9479 (tp) cc_final: 0.9217 (tp) REVERT: A 51 PHE cc_start: 0.9079 (t80) cc_final: 0.8856 (t80) REVERT: A 52 LEU cc_start: 0.9529 (mt) cc_final: 0.9304 (mt) REVERT: A 79 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.8930 (ptm-80) REVERT: A 122 GLN cc_start: 0.8963 (pm20) cc_final: 0.8612 (pm20) REVERT: A 151 HIS cc_start: 0.8608 (m90) cc_final: 0.7888 (m90) REVERT: A 207 ARG cc_start: 0.8743 (tmt170) cc_final: 0.8378 (tpt90) REVERT: A 240 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7867 (mt-10) REVERT: A 263 GLU cc_start: 0.8707 (pp20) cc_final: 0.8453 (pp20) REVERT: A 268 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7494 (p0) REVERT: A 269 TYR cc_start: 0.8439 (m-80) cc_final: 0.7767 (m-80) outliers start: 17 outliers final: 15 residues processed: 207 average time/residue: 0.0553 time to fit residues: 15.0525 Evaluate side-chains 215 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.150018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101249 restraints weight = 7458.850| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 4.19 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4273 Z= 0.182 Angle : 0.878 13.659 5805 Z= 0.424 Chirality : 0.046 0.328 688 Planarity : 0.005 0.065 692 Dihedral : 4.982 43.591 561 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.04 % Allowed : 35.51 % Favored : 60.45 % 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: 2.25 (0.36), residues: 522 helix: 2.21 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -1.30 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 79 TYR 0.021 0.002 TYR B 57 PHE 0.034 0.002 PHE A 196 TRP 0.021 0.002 TRP A 277 HIS 0.004 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 ( 4272) covalent geometry : angle 0.87819 / 0.42 ( 5803) SS BOND : bond 0.00370 / 0.19 ( 1) SS BOND : angle 0.51853 / 0.29 ( 2) hydrogen bonds : bond 0.04018 / 2.57 ( 334) hydrogen bonds : angle 4.36902 / 3.20 ( 1002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.9192 (mtp-110) cc_final: 0.8787 (ttp-110) REVERT: B 82 GLN cc_start: 0.9495 (mm110) cc_final: 0.9085 (tp40) REVERT: B 95 GLN cc_start: 0.9038 (mp10) cc_final: 0.8779 (mp10) REVERT: B 101 ASP cc_start: 0.9630 (t70) cc_final: 0.9273 (m-30) REVERT: B 104 LYS cc_start: 0.9477 (ttmm) cc_final: 0.9227 (mtmm) REVERT: B 231 GLN cc_start: 0.8880 (tt0) cc_final: 0.8353 (tt0) REVERT: B 240 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8079 (pt0) REVERT: A 48 LEU cc_start: 0.9501 (tp) cc_final: 0.9239 (tp) REVERT: A 51 PHE cc_start: 0.9143 (t80) cc_final: 0.8932 (t80) REVERT: A 52 LEU cc_start: 0.9545 (mt) cc_final: 0.9318 (mt) REVERT: A 79 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.8922 (ptm-80) REVERT: A 122 GLN cc_start: 0.8953 (pm20) cc_final: 0.8591 (pm20) REVERT: A 151 HIS cc_start: 0.8652 (m90) cc_final: 0.8148 (m170) REVERT: A 172 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8382 (t80) REVERT: A 207 ARG cc_start: 0.8704 (tmt170) cc_final: 0.8367 (tpt90) REVERT: A 240 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7896 (mt-10) REVERT: A 263 GLU cc_start: 0.8706 (pp20) cc_final: 0.8439 (pp20) REVERT: A 268 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7486 (p0) REVERT: A 269 TYR cc_start: 0.8465 (m-80) cc_final: 0.7733 (m-80) outliers start: 18 outliers final: 15 residues processed: 207 average time/residue: 0.0547 time to fit residues: 14.9151 Evaluate side-chains 217 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 0.0020 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.152293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101970 restraints weight = 7245.357| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.30 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4273 Z= 0.174 Angle : 0.909 14.005 5805 Z= 0.438 Chirality : 0.046 0.337 688 Planarity : 0.005 0.063 692 Dihedral : 4.913 40.825 561 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.37 % Allowed : 37.30 % Favored : 59.33 % 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: 2.22 (0.36), residues: 522 helix: 2.20 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -1.33 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 79 TYR 0.024 0.002 TYR B 270 PHE 0.018 0.001 PHE B 51 TRP 0.020 0.002 TRP A 277 HIS 0.003 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 4272) covalent geometry : angle 0.90947 / 0.44 ( 5803) SS BOND : bond 0.00361 / 0.19 ( 1) SS BOND : angle 0.27075 / 0.16 ( 2) hydrogen bonds : bond 0.03991 / 2.53 ( 334) hydrogen bonds : angle 4.41491 / 3.22 ( 1002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.9182 (mtp-110) cc_final: 0.8879 (ttp-110) REVERT: B 82 GLN cc_start: 0.9492 (mm110) cc_final: 0.9086 (tp40) REVERT: B 95 GLN cc_start: 0.9051 (mp10) cc_final: 0.8821 (mp10) REVERT: B 101 ASP cc_start: 0.9646 (t70) cc_final: 0.9216 (m-30) REVERT: B 104 LYS cc_start: 0.9475 (ttmm) cc_final: 0.9165 (mtmm) REVERT: B 231 GLN cc_start: 0.8864 (tt0) cc_final: 0.8341 (tt0) REVERT: B 240 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7831 (pt0) REVERT: A 48 LEU cc_start: 0.9491 (tp) cc_final: 0.9230 (tp) REVERT: A 51 PHE cc_start: 0.9120 (t80) cc_final: 0.8894 (t80) REVERT: A 52 LEU cc_start: 0.9544 (mt) cc_final: 0.9313 (mt) REVERT: A 79 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.8951 (ptm-80) REVERT: A 122 GLN cc_start: 0.8981 (pm20) cc_final: 0.8604 (pm20) REVERT: A 131 SER cc_start: 0.9558 (t) cc_final: 0.9197 (p) REVERT: A 207 ARG cc_start: 0.8735 (tmt170) cc_final: 0.8357 (tpt90) REVERT: A 240 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7934 (mt-10) REVERT: A 263 GLU cc_start: 0.8720 (pp20) cc_final: 0.8452 (pp20) REVERT: A 268 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7467 (p0) REVERT: A 269 TYR cc_start: 0.8447 (m-80) cc_final: 0.7722 (m-80) outliers start: 15 outliers final: 13 residues processed: 205 average time/residue: 0.0540 time to fit residues: 14.5627 Evaluate side-chains 213 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.151093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101694 restraints weight = 7343.738| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 4.21 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 4273 Z= 0.189 Angle : 0.923 13.989 5805 Z= 0.446 Chirality : 0.046 0.338 688 Planarity : 0.005 0.065 692 Dihedral : 5.051 41.050 561 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.27 % Allowed : 36.63 % Favored : 59.10 % 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: 2.10 (0.36), residues: 522 helix: 2.16 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -1.34 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 79 TYR 0.015 0.002 TYR B 57 PHE 0.052 0.002 PHE A 196 TRP 0.017 0.002 TRP A 277 HIS 0.008 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 ( 4272) covalent geometry : angle 0.92298 / 0.45 ( 5803) SS BOND : bond 0.00308 / 0.16 ( 1) SS BOND : angle 0.23439 / 0.14 ( 2) hydrogen bonds : bond 0.04066 / 2.62 ( 334) hydrogen bonds : angle 4.42588 / 3.24 ( 1002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1099.23 seconds wall clock time: 19 minutes 37.39 seconds (1177.39 seconds total)