Starting phenix.real_space_refine on Tue Aug 4 15:53:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rhe_53967/08_2026/9rhe_53967.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rhe_53967/08_2026/9rhe_53967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rhe_53967/08_2026/9rhe_53967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rhe_53967/08_2026/9rhe_53967.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rhe_53967/08_2026/9rhe_53967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rhe_53967/08_2026/9rhe_53967.map" } resolution = 3.5 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: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2965 2.51 5 N 740 2.21 5 O 826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s 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: 4550 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2827 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 15, 'TRANS': 362} Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 816 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Time building chain proxies: 1.23, per 1000 atoms: 0.27 Number of scatterers: 4550 At special positions: 0 Unit cell: (69.471, 79.515, 100.44, 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 19 16.00 O 826 8.00 N 740 7.00 C 2965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 183.4 milliseconds 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 53.2% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 11 through 31 Processing helix chain 'A' and resid 31 through 44 removed outlier: 4.715A pdb=" N GLY A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TRP A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 85 removed outlier: 3.852A pdb=" N ALA A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 117 removed outlier: 5.073A pdb=" N PHE A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix removed outlier: 3.724A pdb=" N VAL A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.753A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.515A pdb=" N TRP A 126 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA A 127 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.509A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 149 through 175 Processing helix chain 'A' and resid 180 through 200 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.660A pdb=" N TYR A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.505A pdb=" N THR A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 282 through 285 Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.790A pdb=" N VAL A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 333 " --> pdb=" O MET A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 354 through 382 removed outlier: 3.544A pdb=" N VAL A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.680A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.881A pdb=" N PHE C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.641A pdb=" N LYS B 3 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.377A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.597A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.935A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.935A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 786 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: 0.74 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1416 1.35 - 1.46: 1128 1.46 - 1.58: 2075 1.58 - 1.70: 0 1.70 - 1.81: 31 Bond restraints: 4650 Sorted by residual: bond pdb=" CA ASP B 104 " pdb=" CB ASP B 104 " ideal model delta sigma weight residual 1.517 1.550 -0.034 2.41e-02 1.72e+03 1.94e+00 bond pdb=" C THR C 7 " pdb=" N PRO C 8 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.14e+00 bond pdb=" C VAL B 12 " pdb=" N ARG B 13 " ideal model delta sigma weight residual 1.331 1.358 -0.027 2.83e-02 1.25e+03 9.13e-01 bond pdb=" N GLY B 66 " pdb=" CA GLY B 66 " ideal model delta sigma weight residual 1.460 1.443 0.016 1.87e-02 2.86e+03 7.51e-01 bond pdb=" C LYS B 65 " pdb=" N GLY B 66 " ideal model delta sigma weight residual 1.321 1.332 -0.012 1.53e-02 4.27e+03 5.87e-01 ... (remaining 4645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 6244 2.10 - 4.20: 66 4.20 - 6.29: 15 6.29 - 8.39: 1 8.39 - 10.49: 1 Bond angle restraints: 6327 Sorted by residual: angle pdb=" N ILE C 29 " pdb=" CA ILE C 29 " pdb=" C ILE C 29 " ideal model delta sigma weight residual 113.71 110.47 3.24 9.50e-01 1.11e+00 1.16e+01 angle pdb=" CA LEU A 220 " pdb=" CB LEU A 220 " pdb=" CG LEU A 220 " ideal model delta sigma weight residual 116.30 126.79 -10.49 3.50e+00 8.16e-02 8.98e+00 angle pdb=" CA ASP B 104 " pdb=" CB ASP B 104 " pdb=" CG ASP B 104 " ideal model delta sigma weight residual 112.60 115.35 -2.75 1.00e+00 1.00e+00 7.54e+00 angle pdb=" C ALA A 127 " pdb=" N ILE A 128 " pdb=" CA ILE A 128 " ideal model delta sigma weight residual 120.33 122.38 -2.05 8.00e-01 1.56e+00 6.59e+00 angle pdb=" C ILE A 106 " pdb=" N VAL A 107 " pdb=" CA VAL A 107 " ideal model delta sigma weight residual 120.33 122.37 -2.04 8.00e-01 1.56e+00 6.50e+00 ... (remaining 6322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 2404 15.81 - 31.61: 238 31.61 - 47.42: 65 47.42 - 63.22: 16 63.22 - 79.03: 1 Dihedral angle restraints: 2724 sinusoidal: 1010 harmonic: 1714 Sorted by residual: dihedral pdb=" CA GLU B 99 " pdb=" C GLU B 99 " pdb=" N GLU B 100 " pdb=" CA GLU B 100 " ideal model delta harmonic sigma weight residual 180.00 152.83 27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 128.66 -35.66 1 1.00e+01 1.00e-02 1.80e+01 dihedral pdb=" CA ASN B 103 " pdb=" C ASN B 103 " pdb=" N ASP B 104 " pdb=" CA ASP B 104 " ideal model delta harmonic sigma weight residual 180.00 162.23 17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 531 0.033 - 0.067: 164 0.067 - 0.100: 34 0.100 - 0.134: 21 0.134 - 0.167: 1 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA THR C 7 " pdb=" N THR C 7 " pdb=" C THR C 7 " pdb=" CB THR C 7 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA ILE A 237 " pdb=" N ILE A 237 " pdb=" C ILE A 237 " pdb=" CB ILE A 237 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE C 48 " pdb=" N ILE C 48 " pdb=" C ILE C 48 " pdb=" CB ILE C 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 748 not shown) Planarity restraints: 779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 354 " 0.039 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO A 355 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 119 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" CG ASP A 119 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP A 119 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 119 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 41 " -0.008 2.00e-02 2.50e+03 9.79e-03 1.68e+00 pdb=" CG PHE A 41 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 41 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 41 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 41 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 41 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 41 " -0.000 2.00e-02 2.50e+03 ... (remaining 776 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 42 2.63 - 3.20: 4061 3.20 - 3.76: 7085 3.76 - 4.33: 9548 4.33 - 4.90: 16333 Nonbonded interactions: 37069 Sorted by model distance: nonbonded pdb=" OD1 ASP B 104 " pdb=" N PHE B 105 " model vdw 2.062 3.120 nonbonded pdb=" OH TYR A 38 " pdb=" O PHE A 269 " model vdw 2.239 3.040 nonbonded pdb=" OG SER C 34 " pdb=" O ILE C 48 " model vdw 2.242 3.040 nonbonded pdb=" NZ LYS A 57 " pdb=" O LEU A 220 " model vdw 2.256 3.120 nonbonded pdb=" NZ LYS B 19 " pdb=" OE1 GLU B 82 " model vdw 2.302 3.120 ... (remaining 37064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.340 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 0.034 4652 Z= 0.116 Angle : 0.584 10.488 6331 Z= 0.315 Chirality : 0.038 0.167 751 Planarity : 0.004 0.060 779 Dihedral : 13.761 79.027 1626 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.21 % Allowed : 12.86 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.36), residues: 596 helix: 1.21 (0.31), residues: 282 sheet: 1.01 (0.54), residues: 99 loop : -0.29 (0.46), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.007 0.001 TYR C 71 PHE 0.023 0.001 PHE A 41 TRP 0.017 0.001 TRP C 35 HIS 0.003 0.000 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 4650) covalent geometry : angle 0.58358 / 0.32 ( 6327) SS BOND : bond 0.00317 / 0.16 ( 2) SS BOND : angle 0.75380 / 0.55 ( 4) hydrogen bonds : bond 0.23750 / 15.59 ( 275) hydrogen bonds : angle 8.49019 / 6.18 ( 786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.104 Fit side-chains REVERT: A 133 ASP cc_start: 0.7570 (t70) cc_final: 0.7343 (t70) REVERT: B 106 ASP cc_start: 0.6564 (t0) cc_final: 0.6361 (t0) REVERT: C 44 ILE cc_start: 0.6920 (mt) cc_final: 0.6641 (mp) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.0568 time to fit residues: 5.8585 Evaluate side-chains 76 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 HIS A 271 ASN A 277 GLN A 318 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.180062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.134513 restraints weight = 6242.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134969 restraints weight = 5338.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.135780 restraints weight = 5069.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.135963 restraints weight = 3684.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136163 restraints weight = 2992.262| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4652 Z= 0.144 Angle : 0.582 7.176 6331 Z= 0.298 Chirality : 0.040 0.164 751 Planarity : 0.004 0.044 779 Dihedral : 4.195 24.249 641 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.87 % Allowed : 12.03 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.36), residues: 596 helix: 1.68 (0.30), residues: 288 sheet: 1.19 (0.54), residues: 99 loop : -0.32 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.009 0.001 TYR A 38 PHE 0.021 0.001 PHE B 105 TRP 0.012 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 4650) covalent geometry : angle 0.58232 / 0.30 ( 6327) SS BOND : bond 0.00433 / 0.22 ( 2) SS BOND : angle 0.53786 / 0.39 ( 4) hydrogen bonds : bond 0.04752 / 3.19 ( 275) hydrogen bonds : angle 5.52840 / 4.04 ( 786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.170 Fit side-chains REVERT: C 24 ARG cc_start: 0.5922 (tmt-80) cc_final: 0.5604 (tpt90) outliers start: 9 outliers final: 6 residues processed: 84 average time/residue: 0.0622 time to fit residues: 7.0795 Evaluate side-chains 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 103 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.175290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.127245 restraints weight = 6363.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126382 restraints weight = 5664.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126827 restraints weight = 5532.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.127768 restraints weight = 4327.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128010 restraints weight = 3608.273| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4652 Z= 0.130 Angle : 0.545 6.729 6331 Z= 0.278 Chirality : 0.040 0.157 751 Planarity : 0.003 0.037 779 Dihedral : 4.172 21.553 641 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.66 % Allowed : 14.73 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.36), residues: 596 helix: 1.81 (0.31), residues: 285 sheet: 0.84 (0.51), residues: 106 loop : -0.14 (0.47), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.009 0.001 TYR A 38 PHE 0.010 0.001 PHE B 105 TRP 0.010 0.001 TRP A 360 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 4650) covalent geometry : angle 0.54320 / 0.28 ( 6327) SS BOND : bond 0.00217 / 0.10 ( 2) SS BOND : angle 1.65235 / 0.94 ( 4) hydrogen bonds : bond 0.04101 / 2.76 ( 275) hydrogen bonds : angle 5.15166 / 3.79 ( 786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.165 Fit side-chains REVERT: B 81 MET cc_start: 0.3834 (OUTLIER) cc_final: 0.3289 (tpt) REVERT: C 24 ARG cc_start: 0.5969 (tmt-80) cc_final: 0.5733 (tpt90) outliers start: 8 outliers final: 6 residues processed: 85 average time/residue: 0.0480 time to fit residues: 5.5361 Evaluate side-chains 82 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 103 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.0470 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.178665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131516 restraints weight = 6331.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130898 restraints weight = 5373.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.132170 restraints weight = 5227.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132550 restraints weight = 3933.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132595 restraints weight = 3798.682| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4652 Z= 0.102 Angle : 0.532 8.695 6331 Z= 0.266 Chirality : 0.039 0.148 751 Planarity : 0.003 0.034 779 Dihedral : 3.962 20.287 641 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.66 % Allowed : 16.80 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.35), residues: 596 helix: 2.01 (0.31), residues: 284 sheet: 1.19 (0.53), residues: 99 loop : -0.27 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.011 0.001 TYR A 38 PHE 0.012 0.001 PHE B 105 TRP 0.011 0.001 TRP A 360 HIS 0.002 0.000 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 4650) covalent geometry : angle 0.53058 / 0.27 ( 6327) SS BOND : bond 0.00280 / 0.14 ( 2) SS BOND : angle 1.57683 / 0.91 ( 4) hydrogen bonds : bond 0.03431 / 2.30 ( 275) hydrogen bonds : angle 4.85244 / 3.60 ( 786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.105 Fit side-chains REVERT: A 30 ASN cc_start: 0.8231 (m-40) cc_final: 0.8025 (m-40) REVERT: A 181 MET cc_start: 0.7106 (tmm) cc_final: 0.6858 (ppp) REVERT: A 382 VAL cc_start: 0.8949 (m) cc_final: 0.8702 (p) REVERT: C 44 ILE cc_start: 0.6825 (mt) cc_final: 0.6603 (mp) outliers start: 8 outliers final: 6 residues processed: 90 average time/residue: 0.0608 time to fit residues: 7.2919 Evaluate side-chains 83 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.181041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.134408 restraints weight = 6305.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134655 restraints weight = 5342.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.135817 restraints weight = 4752.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135795 restraints weight = 3613.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135998 restraints weight = 2963.084| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4652 Z= 0.107 Angle : 0.531 6.749 6331 Z= 0.268 Chirality : 0.038 0.147 751 Planarity : 0.003 0.032 779 Dihedral : 3.928 18.972 641 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.87 % Allowed : 16.80 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.35), residues: 596 helix: 2.01 (0.31), residues: 284 sheet: 1.18 (0.53), residues: 99 loop : -0.27 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.011 0.001 TYR A 38 PHE 0.013 0.001 PHE B 105 TRP 0.012 0.001 TRP A 360 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 4650) covalent geometry : angle 0.52998 / 0.27 ( 6327) SS BOND : bond 0.00285 / 0.14 ( 2) SS BOND : angle 1.39022 / 0.83 ( 4) hydrogen bonds : bond 0.03368 / 2.25 ( 275) hydrogen bonds : angle 4.74628 / 3.52 ( 786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.169 Fit side-chains REVERT: A 30 ASN cc_start: 0.8199 (m-40) cc_final: 0.7995 (m-40) REVERT: A 181 MET cc_start: 0.7030 (tmm) cc_final: 0.6827 (ppp) REVERT: A 228 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8558 (mt) REVERT: C 44 ILE cc_start: 0.6877 (mt) cc_final: 0.6670 (mp) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.0646 time to fit residues: 7.4625 Evaluate side-chains 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.181009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134011 restraints weight = 6420.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134467 restraints weight = 5272.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.135008 restraints weight = 4904.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.135464 restraints weight = 3469.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135638 restraints weight = 2867.211| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4652 Z= 0.115 Angle : 0.543 6.758 6331 Z= 0.274 Chirality : 0.040 0.253 751 Planarity : 0.003 0.030 779 Dihedral : 3.939 18.696 641 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.28 % Allowed : 16.60 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.35), residues: 596 helix: 2.02 (0.31), residues: 284 sheet: 1.14 (0.52), residues: 99 loop : -0.26 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 383 TYR 0.010 0.001 TYR A 38 PHE 0.013 0.001 PHE B 105 TRP 0.017 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 ( 4650) covalent geometry : angle 0.54170 / 0.27 ( 6327) SS BOND : bond 0.00288 / 0.14 ( 2) SS BOND : angle 1.33390 / 0.80 ( 4) hydrogen bonds : bond 0.03342 / 2.25 ( 275) hydrogen bonds : angle 4.69650 / 3.49 ( 786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.167 Fit side-chains REVERT: A 228 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8561 (mt) REVERT: C 44 ILE cc_start: 0.6895 (mt) cc_final: 0.6688 (mp) outliers start: 11 outliers final: 10 residues processed: 87 average time/residue: 0.0616 time to fit residues: 7.2080 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.176260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126758 restraints weight = 6341.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127846 restraints weight = 5448.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128148 restraints weight = 4597.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.128386 restraints weight = 3448.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128567 restraints weight = 2858.528| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4652 Z= 0.130 Angle : 0.559 6.568 6331 Z= 0.283 Chirality : 0.040 0.202 751 Planarity : 0.003 0.028 779 Dihedral : 4.010 19.874 641 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.07 % Allowed : 17.84 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.35), residues: 596 helix: 2.01 (0.31), residues: 284 sheet: 1.05 (0.52), residues: 99 loop : -0.25 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.010 0.001 TYR A 38 PHE 0.016 0.001 PHE B 29 TRP 0.013 0.001 TRP A 360 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 4650) covalent geometry : angle 0.55808 / 0.28 ( 6327) SS BOND : bond 0.00356 / 0.17 ( 2) SS BOND : angle 1.32791 / 0.83 ( 4) hydrogen bonds : bond 0.03439 / 2.31 ( 275) hydrogen bonds : angle 4.71392 / 3.51 ( 786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.167 Fit side-chains REVERT: C 44 ILE cc_start: 0.6949 (mt) cc_final: 0.6712 (mp) outliers start: 10 outliers final: 10 residues processed: 86 average time/residue: 0.0666 time to fit residues: 7.5611 Evaluate side-chains 85 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.183112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136406 restraints weight = 6302.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138782 restraints weight = 6045.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139435 restraints weight = 4245.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139411 restraints weight = 3445.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139814 restraints weight = 2871.792| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4652 Z= 0.114 Angle : 0.554 6.932 6331 Z= 0.282 Chirality : 0.039 0.153 751 Planarity : 0.003 0.028 779 Dihedral : 3.946 19.198 641 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.28 % Allowed : 17.84 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.35), residues: 596 helix: 2.03 (0.31), residues: 284 sheet: 1.06 (0.52), residues: 99 loop : -0.24 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.017 0.001 TYR A 208 PHE 0.017 0.001 PHE B 105 TRP 0.013 0.001 TRP A 360 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 4650) covalent geometry : angle 0.55338 / 0.28 ( 6327) SS BOND : bond 0.00334 / 0.16 ( 2) SS BOND : angle 1.27315 / 0.77 ( 4) hydrogen bonds : bond 0.03236 / 2.17 ( 275) hydrogen bonds : angle 4.63005 / 3.45 ( 786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.170 Fit side-chains REVERT: A 228 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8616 (mt) REVERT: C 44 ILE cc_start: 0.6991 (mt) cc_final: 0.6779 (mp) outliers start: 11 outliers final: 10 residues processed: 87 average time/residue: 0.0654 time to fit residues: 7.6138 Evaluate side-chains 85 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.184000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136669 restraints weight = 6219.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.138475 restraints weight = 5764.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139104 restraints weight = 3923.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.139269 restraints weight = 2812.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139564 restraints weight = 2612.843| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4652 Z= 0.136 Angle : 0.579 6.901 6331 Z= 0.295 Chirality : 0.040 0.149 751 Planarity : 0.003 0.027 779 Dihedral : 4.040 20.776 641 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.28 % Allowed : 18.05 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.35), residues: 596 helix: 2.00 (0.31), residues: 284 sheet: 1.19 (0.52), residues: 97 loop : -0.23 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.015 0.002 TYR B 107 PHE 0.014 0.001 PHE B 105 TRP 0.013 0.001 TRP A 360 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 4650) covalent geometry : angle 0.57785 / 0.30 ( 6327) SS BOND : bond 0.00329 / 0.16 ( 2) SS BOND : angle 1.25730 / 0.77 ( 4) hydrogen bonds : bond 0.03424 / 2.30 ( 275) hydrogen bonds : angle 4.66096 / 3.48 ( 786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.173 Fit side-chains REVERT: A 181 MET cc_start: 0.6463 (ppp) cc_final: 0.5937 (mtm) REVERT: A 228 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8613 (mt) REVERT: C 44 ILE cc_start: 0.7014 (mt) cc_final: 0.6774 (mp) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.0595 time to fit residues: 6.8147 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.0770 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.186003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.139565 restraints weight = 6199.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140435 restraints weight = 5944.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142098 restraints weight = 3929.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142125 restraints weight = 2893.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142391 restraints weight = 2549.896| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 4652 Z= 0.109 Angle : 0.561 7.171 6331 Z= 0.284 Chirality : 0.039 0.139 751 Planarity : 0.003 0.028 779 Dihedral : 3.890 21.744 641 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.87 % Allowed : 18.46 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.35), residues: 596 helix: 2.14 (0.31), residues: 282 sheet: 1.06 (0.52), residues: 99 loop : -0.12 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 24 TYR 0.012 0.001 TYR B 107 PHE 0.017 0.001 PHE B 105 TRP 0.013 0.001 TRP A 360 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 4650) covalent geometry : angle 0.55965 / 0.28 ( 6327) SS BOND : bond 0.00316 / 0.15 ( 2) SS BOND : angle 1.61154 / 0.93 ( 4) hydrogen bonds : bond 0.03089 / 2.07 ( 275) hydrogen bonds : angle 4.51967 / 3.38 ( 786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.6394 (ppp) cc_final: 0.5847 (mtm) REVERT: A 228 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8574 (mt) REVERT: C 44 ILE cc_start: 0.6928 (mt) cc_final: 0.6728 (mp) outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 0.0503 time to fit residues: 6.0769 Evaluate side-chains 85 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.182714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134678 restraints weight = 6292.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136213 restraints weight = 5741.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136597 restraints weight = 3739.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137060 restraints weight = 3059.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137287 restraints weight = 2533.886| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4652 Z= 0.112 Angle : 0.574 7.130 6331 Z= 0.289 Chirality : 0.039 0.143 751 Planarity : 0.003 0.029 779 Dihedral : 3.896 22.223 641 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.87 % Allowed : 19.50 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.35), residues: 596 helix: 2.07 (0.31), residues: 285 sheet: 1.04 (0.52), residues: 99 loop : -0.12 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 24 TYR 0.011 0.001 TYR A 208 PHE 0.016 0.001 PHE B 105 TRP 0.012 0.001 TRP A 360 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 4650) covalent geometry : angle 0.57302 / 0.29 ( 6327) SS BOND : bond 0.00319 / 0.15 ( 2) SS BOND : angle 1.47394 / 0.87 ( 4) hydrogen bonds : bond 0.03129 / 2.10 ( 275) hydrogen bonds : angle 4.52428 / 3.39 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 926.99 seconds wall clock time: 16 minutes 38.35 seconds (998.35 seconds total)