Starting phenix.real_space_refine on Tue Aug 4 13:17:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12oy_76655/08_2026/12oy_76655.cif Found real_map, /net/cci-nas-00/data/ceres_data/12oy_76655/08_2026/12oy_76655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12oy_76655/08_2026/12oy_76655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12oy_76655/08_2026/12oy_76655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12oy_76655/08_2026/12oy_76655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12oy_76655/08_2026/12oy_76655.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 2048 2.51 5 N 539 2.21 5 O 575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3186 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 285, 2207 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 285, 2207 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 2245 Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 201 " occ=0.63 ... (22 atoms not shown) pdb=" OH BTYR A 201 " occ=0.37 Time building chain proxies: 0.84, per 1000 atoms: 0.26 Number of scatterers: 3186 At special positions: 0 Unit cell: (72.384, 68.224, 104, 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 575 8.00 N 539 7.00 C 2048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 98 " 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: 0.14 Conformation dependent library (CDL) restraints added in 112.5 milliseconds 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 4 sheets defined 55.4% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Proline residue: A 20 - end of helix Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 73 through 99 removed outlier: 3.603A pdb=" N ARG A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 150 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 151 through 154 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.585A pdb=" N PHE A 179 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 210 removed outlier: 3.821A pdb=" N ARG A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 235 Processing helix chain 'A' and resid 235 through 248 removed outlier: 3.860A pdb=" N VAL A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.135A pdb=" N THR B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 removed outlier: 3.701A pdb=" N LYS B 67 " --> pdb=" O ASP B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 108 through 114 removed outlier: 3.557A pdb=" N TYR B 112 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 Processing sheet with id=AA2, first strand: chain 'B' and resid 8 through 10 Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.672A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA B 53 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N MET B 37 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.672A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA B 53 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N MET B 37 " --> pdb=" O ALA B 53 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 571 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: 0.46 Time building geometry restraints manager: 0.20 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: 1012 1.34 - 1.46: 804 1.46 - 1.58: 1415 1.58 - 1.70: 0 1.70 - 1.81: 34 Bond restraints: 3265 Sorted by residual: bond pdb=" CA PRO A 36 " pdb=" C PRO A 36 " ideal model delta sigma weight residual 1.517 1.513 0.004 6.70e-03 2.23e+04 4.23e-01 bond pdb=" C VAL A 217 " pdb=" N PRO A 218 " ideal model delta sigma weight residual 1.335 1.344 -0.008 1.36e-02 5.41e+03 3.78e-01 bond pdb=" C GLN A 19 " pdb=" N PRO A 20 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.36e-02 5.41e+03 3.39e-01 bond pdb=" C SER A 98 " pdb=" N ASP A 99 " ideal model delta sigma weight residual 1.329 1.336 -0.007 1.40e-02 5.10e+03 2.64e-01 bond pdb=" CA LEU A 285 " pdb=" CB LEU A 285 " ideal model delta sigma weight residual 1.530 1.539 -0.008 1.69e-02 3.50e+03 2.49e-01 ... (remaining 3260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 4339 1.29 - 2.58: 68 2.58 - 3.86: 15 3.86 - 5.15: 8 5.15 - 6.44: 2 Bond angle restraints: 4432 Sorted by residual: angle pdb=" N LYS A 158 " pdb=" CA LYS A 158 " pdb=" C LYS A 158 " ideal model delta sigma weight residual 114.75 110.68 4.07 1.26e+00 6.30e-01 1.05e+01 angle pdb=" C LYS B 78 " pdb=" N ASN B 79 " pdb=" CA ASN B 79 " ideal model delta sigma weight residual 121.54 125.72 -4.18 1.91e+00 2.74e-01 4.80e+00 angle pdb=" CA LYS A 158 " pdb=" C LYS A 158 " pdb=" N TYR A 159 " ideal model delta sigma weight residual 119.80 116.93 2.87 1.34e+00 5.57e-01 4.60e+00 angle pdb=" CA LEU A 17 " pdb=" CB LEU A 17 " pdb=" CG LEU A 17 " ideal model delta sigma weight residual 116.30 122.74 -6.44 3.50e+00 8.16e-02 3.39e+00 angle pdb=" CA LYS A 158 " pdb=" C LYS A 158 " pdb=" O LYS A 158 " ideal model delta sigma weight residual 118.47 120.50 -2.03 1.14e+00 7.69e-01 3.18e+00 ... (remaining 4427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 1818 17.16 - 34.32: 85 34.32 - 51.48: 13 51.48 - 68.64: 1 68.64 - 85.80: 2 Dihedral angle restraints: 1919 sinusoidal: 742 harmonic: 1177 Sorted by residual: dihedral pdb=" N LEU A 74 " pdb=" CA LEU A 74 " pdb=" CB LEU A 74 " pdb=" CG LEU A 74 " ideal model delta sinusoidal sigma weight residual -60.00 -112.38 52.38 3 1.50e+01 4.44e-03 9.11e+00 dihedral pdb=" N ARG B 69 " pdb=" CA ARG B 69 " pdb=" CB ARG B 69 " pdb=" CG ARG B 69 " ideal model delta sinusoidal sigma weight residual -60.00 -102.46 42.46 3 1.50e+01 4.44e-03 7.62e+00 dihedral pdb=" CA TYR A 32 " pdb=" CB TYR A 32 " pdb=" CG TYR A 32 " pdb=" CD1 TYR A 32 " ideal model delta sinusoidal sigma weight residual 90.00 38.74 51.26 2 2.00e+01 2.50e-03 7.30e+00 ... (remaining 1916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 274 0.024 - 0.048: 139 0.048 - 0.073: 51 0.073 - 0.097: 19 0.097 - 0.121: 9 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL B 127 " pdb=" N VAL B 127 " pdb=" C VAL B 127 " pdb=" CB VAL B 127 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA VAL B 95 " pdb=" N VAL B 95 " pdb=" C VAL B 95 " pdb=" CB VAL B 95 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA VAL A 290 " pdb=" N VAL A 290 " pdb=" C VAL A 290 " pdb=" CB VAL A 290 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.91e-01 ... (remaining 489 not shown) Planarity restraints: 562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 125 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO B 126 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 236 " -0.016 5.00e-02 4.00e+02 2.37e-02 8.95e-01 pdb=" N PRO A 237 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 43 " 0.013 5.00e-02 4.00e+02 1.94e-02 6.01e-01 pdb=" N PRO B 44 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " 0.011 5.00e-02 4.00e+02 ... (remaining 559 not shown) Histogram of nonbonded interaction distances: 2.65 - 3.10: 2313 3.10 - 3.55: 3493 3.55 - 4.00: 4568 4.00 - 4.45: 5652 4.45 - 4.90: 8620 Nonbonded interactions: 24646 Sorted by model distance: nonbonded pdb=" N ASP A 216 " pdb=" O ASP A 216 " model vdw 2.647 2.496 nonbonded pdb=" N SER B 73 " pdb=" O SER B 73 " model vdw 2.650 2.496 nonbonded pdb=" N ALA B 94 " pdb=" O ALA B 94 " model vdw 2.662 2.496 nonbonded pdb=" N VAL A 48 " pdb=" O VAL A 48 " model vdw 2.664 2.496 nonbonded pdb=" CB ALA A 2 " pdb=" N ASP A 3 " model vdw 2.665 2.832 ... (remaining 24641 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=0.37 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: 13.370 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: 4.170 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 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 : 0.002 0.017 3266 Z= 0.093 Angle : 0.483 6.440 4434 Z= 0.246 Chirality : 0.036 0.121 492 Planarity : 0.003 0.027 562 Dihedral : 10.011 85.803 1170 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.58 % Allowed : 5.54 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.17 (0.44), residues: 407 helix: 3.53 (0.37), residues: 194 sheet: -0.00 (0.73), residues: 42 loop : 1.08 (0.54), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 288 TYR 0.007 0.001 TYR B 97 PHE 0.005 0.001 PHE B 40 TRP 0.006 0.001 TRP A 266 HIS 0.001 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00165 / 0.09 ( 3265) covalent geometry : angle 0.48340 / 0.25 ( 4432) SS BOND : bond 0.00036 / 0.02 ( 1) SS BOND : angle 0.55715 / 0.37 ( 2) hydrogen bonds : bond 0.13379 / 8.88 ( 197) hydrogen bonds : angle 5.91588 / 3.86 ( 571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.8945 (tmm) cc_final: 0.8646 (tmm) REVERT: A 149 MET cc_start: 0.9423 (ttm) cc_final: 0.8673 (ttm) REVERT: A 233 MET cc_start: 0.8558 (tmm) cc_final: 0.8345 (tmm) REVERT: A 275 LYS cc_start: 0.9469 (ptpt) cc_final: 0.9134 (mtmm) REVERT: A 279 MET cc_start: 0.7659 (ttp) cc_final: 0.7289 (ttp) outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.0827 time to fit residues: 4.9997 Evaluate side-chains 34 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.0370 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.072307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.048751 restraints weight = 40440.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.051393 restraints weight = 9383.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.053267 restraints weight = 4641.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054436 restraints weight = 3103.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.055287 restraints weight = 2443.929| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3266 Z= 0.125 Angle : 0.551 6.010 4434 Z= 0.270 Chirality : 0.038 0.143 492 Planarity : 0.003 0.028 562 Dihedral : 3.036 13.117 455 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.87 % Allowed : 10.20 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.30 (0.44), residues: 407 helix: 3.55 (0.36), residues: 194 sheet: 0.47 (0.72), residues: 42 loop : 1.12 (0.54), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 288 TYR 0.011 0.001 TYR B 120 PHE 0.010 0.001 PHE B 50 TRP 0.009 0.001 TRP A 194 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 3265) covalent geometry : angle 0.55068 / 0.27 ( 4432) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 0.22318 / 0.15 ( 2) hydrogen bonds : bond 0.03179 / 2.14 ( 197) hydrogen bonds : angle 4.35260 / 2.96 ( 571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.9078 (tmm) cc_final: 0.8725 (tmm) REVERT: A 149 MET cc_start: 0.9615 (ttm) cc_final: 0.9020 (ttm) REVERT: A 233 MET cc_start: 0.8702 (tmm) cc_final: 0.8443 (tmm) REVERT: A 272 MET cc_start: 0.8797 (mmp) cc_final: 0.8549 (mmp) REVERT: A 275 LYS cc_start: 0.9437 (ptpt) cc_final: 0.9224 (mtmm) REVERT: A 279 MET cc_start: 0.7746 (ttp) cc_final: 0.7275 (ttp) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.0762 time to fit residues: 3.7332 Evaluate side-chains 38 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 169 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN A 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.071419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.048301 restraints weight = 36087.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.050856 restraints weight = 8899.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052642 restraints weight = 4535.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053721 restraints weight = 3077.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.054558 restraints weight = 2468.855| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3266 Z= 0.154 Angle : 0.554 7.694 4434 Z= 0.270 Chirality : 0.038 0.118 492 Planarity : 0.003 0.029 562 Dihedral : 3.140 13.624 455 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.17 % Allowed : 10.20 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.24 (0.43), residues: 407 helix: 3.53 (0.35), residues: 194 sheet: 0.29 (0.71), residues: 42 loop : 1.10 (0.53), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 30 TYR 0.024 0.001 TYR B 120 PHE 0.009 0.001 PHE B 50 TRP 0.007 0.001 TRP A 194 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 3265) covalent geometry : angle 0.55404 / 0.27 ( 4432) SS BOND : bond 0.00032 / 0.02 ( 1) SS BOND : angle 0.19624 / 0.13 ( 2) hydrogen bonds : bond 0.02981 / 2.03 ( 197) hydrogen bonds : angle 4.09676 / 2.82 ( 571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.9066 (tmm) cc_final: 0.8731 (tmm) REVERT: A 149 MET cc_start: 0.9637 (ttm) cc_final: 0.9088 (ttm) REVERT: A 233 MET cc_start: 0.8703 (tmm) cc_final: 0.8452 (tmm) REVERT: A 272 MET cc_start: 0.8860 (mmp) cc_final: 0.8582 (mmp) REVERT: A 275 LYS cc_start: 0.9446 (ptpt) cc_final: 0.9214 (mtmm) REVERT: A 279 MET cc_start: 0.7734 (ttp) cc_final: 0.7287 (ttp) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.0745 time to fit residues: 3.6515 Evaluate side-chains 36 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 169 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.071026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.048321 restraints weight = 27409.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.050753 restraints weight = 7946.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.052450 restraints weight = 4254.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053448 restraints weight = 2967.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.054249 restraints weight = 2418.777| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3266 Z= 0.174 Angle : 0.553 6.835 4434 Z= 0.273 Chirality : 0.038 0.119 492 Planarity : 0.003 0.030 562 Dihedral : 3.206 14.363 455 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.75 % Allowed : 11.37 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.16 (0.43), residues: 407 helix: 3.48 (0.35), residues: 194 sheet: 0.12 (0.70), residues: 42 loop : 1.08 (0.53), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 5 TYR 0.026 0.001 TYR B 120 PHE 0.009 0.001 PHE B 50 TRP 0.006 0.001 TRP A 194 HIS 0.002 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 3265) covalent geometry : angle 0.55345 / 0.27 ( 4432) SS BOND : bond 0.00053 / 0.03 ( 1) SS BOND : angle 0.09988 / 0.07 ( 2) hydrogen bonds : bond 0.02923 / 1.98 ( 197) hydrogen bonds : angle 4.01276 / 2.77 ( 571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.9079 (tmm) cc_final: 0.8730 (tmm) REVERT: A 33 GLU cc_start: 0.8848 (mp0) cc_final: 0.8585 (pm20) REVERT: A 149 MET cc_start: 0.9638 (ttm) cc_final: 0.9088 (ttm) REVERT: A 233 MET cc_start: 0.8706 (tmm) cc_final: 0.8455 (tmm) REVERT: A 279 MET cc_start: 0.7708 (ttp) cc_final: 0.7264 (ttp) outliers start: 6 outliers final: 3 residues processed: 44 average time/residue: 0.0678 time to fit residues: 3.6762 Evaluate side-chains 39 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.0020 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 ASN ** 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 = 0.3443 r_free = 0.3443 target = 0.071818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.048714 restraints weight = 38141.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.051305 restraints weight = 9114.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.053138 restraints weight = 4594.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.054345 restraints weight = 3112.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.055015 restraints weight = 2459.046| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3266 Z= 0.134 Angle : 0.564 6.634 4434 Z= 0.276 Chirality : 0.037 0.117 492 Planarity : 0.003 0.031 562 Dihedral : 3.145 12.933 455 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.87 % Allowed : 12.83 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.16 (0.43), residues: 407 helix: 3.49 (0.35), residues: 194 sheet: 0.10 (0.69), residues: 42 loop : 1.07 (0.53), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 5 TYR 0.010 0.001 TYR B 120 PHE 0.010 0.001 PHE B 50 TRP 0.007 0.001 TRP A 194 HIS 0.002 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 3265) covalent geometry : angle 0.56398 / 0.28 ( 4432) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 0.11526 / 0.08 ( 2) hydrogen bonds : bond 0.02817 / 1.89 ( 197) hydrogen bonds : angle 3.91157 / 2.71 ( 571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.9064 (tmm) cc_final: 0.8715 (tmm) REVERT: A 33 GLU cc_start: 0.8853 (mp0) cc_final: 0.8610 (pm20) REVERT: A 149 MET cc_start: 0.9631 (ttm) cc_final: 0.9140 (ttm) REVERT: A 233 MET cc_start: 0.8700 (tmm) cc_final: 0.8457 (tmm) REVERT: A 279 MET cc_start: 0.7710 (ttp) cc_final: 0.7274 (ttp) outliers start: 3 outliers final: 3 residues processed: 40 average time/residue: 0.0768 time to fit residues: 3.7578 Evaluate side-chains 38 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.070782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.047719 restraints weight = 38038.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.050239 restraints weight = 9108.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.052004 restraints weight = 4620.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.053199 restraints weight = 3149.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.053854 restraints weight = 2492.808| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3266 Z= 0.199 Angle : 0.593 5.922 4434 Z= 0.294 Chirality : 0.038 0.121 492 Planarity : 0.004 0.038 562 Dihedral : 3.240 15.091 455 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.17 % Allowed : 14.29 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.05 (0.42), residues: 407 helix: 3.37 (0.35), residues: 194 sheet: 0.06 (0.69), residues: 42 loop : 1.06 (0.52), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.010 0.001 TYR B 97 PHE 0.010 0.001 PHE B 50 TRP 0.005 0.001 TRP A 194 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 ( 3265) covalent geometry : angle 0.59292 / 0.29 ( 4432) SS BOND : bond 0.00011 / 0.01 ( 1) SS BOND : angle 0.13155 / 0.09 ( 2) hydrogen bonds : bond 0.02982 / 2.01 ( 197) hydrogen bonds : angle 3.99618 / 2.77 ( 571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.9093 (tmm) cc_final: 0.8716 (tmm) REVERT: A 33 GLU cc_start: 0.8812 (mp0) cc_final: 0.8582 (pm20) REVERT: A 149 MET cc_start: 0.9632 (ttm) cc_final: 0.9076 (ttm) REVERT: A 233 MET cc_start: 0.8686 (tmm) cc_final: 0.8460 (tmm) REVERT: A 279 MET cc_start: 0.7736 (ttp) cc_final: 0.7314 (ttp) outliers start: 4 outliers final: 4 residues processed: 41 average time/residue: 0.0896 time to fit residues: 4.3948 Evaluate side-chains 40 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 ASN ** 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 = 0.3432 r_free = 0.3432 target = 0.071404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.048754 restraints weight = 31623.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051256 restraints weight = 8515.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.053018 restraints weight = 4439.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.054157 restraints weight = 3048.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.054879 restraints weight = 2422.464| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3266 Z= 0.137 Angle : 0.595 6.500 4434 Z= 0.292 Chirality : 0.037 0.123 492 Planarity : 0.003 0.032 562 Dihedral : 3.164 13.046 455 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.17 % Allowed : 14.29 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.10 (0.43), residues: 407 helix: 3.38 (0.35), residues: 194 sheet: 0.09 (0.70), residues: 42 loop : 1.11 (0.53), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 30 TYR 0.013 0.001 TYR A 263 PHE 0.009 0.001 PHE B 50 TRP 0.007 0.001 TRP A 270 HIS 0.001 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 3265) covalent geometry : angle 0.59502 / 0.29 ( 4432) SS BOND : bond 0.00071 / 0.04 ( 1) SS BOND : angle 0.15235 / 0.10 ( 2) hydrogen bonds : bond 0.02790 / 1.87 ( 197) hydrogen bonds : angle 3.91313 / 2.72 ( 571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.9094 (tmm) cc_final: 0.8709 (tmm) REVERT: A 33 GLU cc_start: 0.8805 (mp0) cc_final: 0.8573 (pm20) REVERT: A 149 MET cc_start: 0.9617 (ttm) cc_final: 0.9027 (ttm) REVERT: A 233 MET cc_start: 0.8693 (tmm) cc_final: 0.8473 (tmm) REVERT: A 279 MET cc_start: 0.7686 (ttp) cc_final: 0.7235 (ttp) REVERT: B 61 TYR cc_start: 0.8472 (m-10) cc_final: 0.8135 (m-10) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.0833 time to fit residues: 4.4354 Evaluate side-chains 39 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 ASN ** 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 = 0.3408 r_free = 0.3408 target = 0.070652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.047738 restraints weight = 47079.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.050310 restraints weight = 9719.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.052189 restraints weight = 4691.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.053430 restraints weight = 3083.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.054138 restraints weight = 2397.093| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3266 Z= 0.168 Angle : 0.608 8.055 4434 Z= 0.297 Chirality : 0.038 0.118 492 Planarity : 0.004 0.032 562 Dihedral : 3.199 13.895 455 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.75 % Allowed : 14.29 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.01 (0.43), residues: 407 helix: 3.31 (0.35), residues: 194 sheet: 0.02 (0.70), residues: 42 loop : 1.08 (0.53), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 30 TYR 0.011 0.001 TYR A 263 PHE 0.009 0.001 PHE B 70 TRP 0.009 0.001 TRP A 194 HIS 0.002 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 3265) covalent geometry : angle 0.60802 / 0.30 ( 4432) SS BOND : bond 0.00024 / 0.01 ( 1) SS BOND : angle 0.17587 / 0.12 ( 2) hydrogen bonds : bond 0.02884 / 1.94 ( 197) hydrogen bonds : angle 3.90069 / 2.70 ( 571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.9095 (tmm) cc_final: 0.8702 (tmm) REVERT: A 33 GLU cc_start: 0.8788 (mp0) cc_final: 0.8554 (pm20) REVERT: A 149 MET cc_start: 0.9619 (ttm) cc_final: 0.9041 (ttm) REVERT: A 233 MET cc_start: 0.8700 (tmm) cc_final: 0.8460 (tmm) REVERT: A 279 MET cc_start: 0.7648 (ttp) cc_final: 0.7195 (ttp) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.0780 time to fit residues: 3.8893 Evaluate side-chains 39 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 0.0070 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.071188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.048322 restraints weight = 43350.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.050923 restraints weight = 9511.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.052769 restraints weight = 4665.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053951 restraints weight = 3122.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.054807 restraints weight = 2442.990| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3266 Z= 0.133 Angle : 0.638 8.191 4434 Z= 0.307 Chirality : 0.037 0.118 492 Planarity : 0.004 0.033 562 Dihedral : 3.157 12.350 455 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.17 % Allowed : 14.87 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.02 (0.43), residues: 407 helix: 3.31 (0.35), residues: 194 sheet: 0.10 (0.70), residues: 42 loop : 1.08 (0.53), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 30 TYR 0.011 0.001 TYR A 263 PHE 0.009 0.001 PHE B 50 TRP 0.009 0.001 TRP A 194 HIS 0.001 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 3265) covalent geometry : angle 0.63812 / 0.31 ( 4432) SS BOND : bond 0.00041 / 0.02 ( 1) SS BOND : angle 0.16914 / 0.11 ( 2) hydrogen bonds : bond 0.02774 / 1.85 ( 197) hydrogen bonds : angle 3.82853 / 2.65 ( 571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.146 Fit side-chains REVERT: A 22 MET cc_start: 0.9085 (tmm) cc_final: 0.8693 (tmm) REVERT: A 33 GLU cc_start: 0.8805 (mp0) cc_final: 0.8556 (pm20) REVERT: A 149 MET cc_start: 0.9612 (ttm) cc_final: 0.9040 (ttm) REVERT: A 233 MET cc_start: 0.8688 (tmm) cc_final: 0.8461 (tmm) REVERT: A 279 MET cc_start: 0.7590 (ttp) cc_final: 0.7121 (ttp) REVERT: B 61 TYR cc_start: 0.8452 (m-10) cc_final: 0.8144 (m-10) outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.0783 time to fit residues: 3.9841 Evaluate side-chains 39 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 ASN ** 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 = 0.3404 r_free = 0.3404 target = 0.070515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.047392 restraints weight = 53794.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.049989 restraints weight = 10384.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.051858 restraints weight = 4949.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.053062 restraints weight = 3256.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053922 restraints weight = 2540.297| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3266 Z= 0.170 Angle : 0.623 7.322 4434 Z= 0.306 Chirality : 0.038 0.118 492 Planarity : 0.004 0.032 562 Dihedral : 3.198 13.427 455 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.17 % Allowed : 15.45 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.01 (0.43), residues: 407 helix: 3.29 (0.35), residues: 194 sheet: 0.05 (0.70), residues: 42 loop : 1.09 (0.53), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 30 TYR 0.009 0.001 TYR A 263 PHE 0.009 0.001 PHE B 50 TRP 0.007 0.001 TRP A 194 HIS 0.002 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 3265) covalent geometry : angle 0.62319 / 0.31 ( 4432) SS BOND : bond 0.00012 / 0.01 ( 1) SS BOND : angle 0.13918 / 0.09 ( 2) hydrogen bonds : bond 0.02850 / 1.92 ( 197) hydrogen bonds : angle 3.86573 / 2.68 ( 571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.122 Fit side-chains REVERT: A 22 MET cc_start: 0.9105 (tmm) cc_final: 0.8707 (tmm) REVERT: A 33 GLU cc_start: 0.8828 (mp0) cc_final: 0.8577 (pm20) REVERT: A 149 MET cc_start: 0.9621 (ttm) cc_final: 0.9064 (ttm) REVERT: A 233 MET cc_start: 0.8692 (tmm) cc_final: 0.8456 (tmm) REVERT: A 279 MET cc_start: 0.7640 (ttp) cc_final: 0.7169 (ttp) REVERT: B 61 TYR cc_start: 0.8485 (m-10) cc_final: 0.8175 (m-10) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.0690 time to fit residues: 3.2734 Evaluate side-chains 37 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** 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 = 0.3405 r_free = 0.3405 target = 0.070555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.047790 restraints weight = 36367.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.050280 restraints weight = 8993.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.052085 restraints weight = 4565.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.053270 restraints weight = 3097.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053978 restraints weight = 2438.787| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3266 Z= 0.159 Angle : 0.655 8.573 4434 Z= 0.317 Chirality : 0.037 0.121 492 Planarity : 0.004 0.032 562 Dihedral : 3.196 13.210 455 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.17 % Allowed : 15.74 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.02 (0.43), residues: 407 helix: 3.28 (0.35), residues: 194 sheet: 0.01 (0.70), residues: 42 loop : 1.13 (0.54), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 30 TYR 0.011 0.001 TYR A 263 PHE 0.009 0.001 PHE B 50 TRP 0.007 0.001 TRP A 194 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 3265) covalent geometry : angle 0.65540 / 0.32 ( 4432) SS BOND : bond 0.00018 / 0.01 ( 1) SS BOND : angle 0.15370 / 0.10 ( 2) hydrogen bonds : bond 0.02801 / 1.87 ( 197) hydrogen bonds : angle 3.85565 / 2.67 ( 571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1025.85 seconds wall clock time: 18 minutes 22.19 seconds (1102.19 seconds total)