Starting phenix.real_space_refine on Tue Feb 3 16:05:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qia_13985/02_2026/7qia_13985.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qia_13985/02_2026/7qia_13985.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/7qia_13985/02_2026/7qia_13985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qia_13985/02_2026/7qia_13985.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qia_13985/02_2026/7qia_13985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qia_13985/02_2026/7qia_13985.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= 0.001 sd= 0.068 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 28 5.16 5 C 3148 2.51 5 N 809 2.21 5 O 858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4843 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2991 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 12, 'TRANS': 388} Chain: "C" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 1.35, per 1000 atoms: 0.28 Number of scatterers: 4843 At special positions: 0 Unit cell: (88.536, 106.764, 75.516, 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 28 16.00 O 858 8.00 N 809 7.00 C 3148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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: 0.39 Conformation dependent library (CDL) restraints added in 324.3 milliseconds 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 55.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.929A pdb=" N VAL A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 removed outlier: 4.281A pdb=" N THR A 73 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 removed outlier: 4.123A pdb=" N ILE A 79 " --> pdb=" O TRP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 111 through 143 Processing helix chain 'A' and resid 151 through 165 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.976A pdb=" N VAL A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 192 removed outlier: 4.321A pdb=" N THR A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 227 through 242 removed outlier: 4.203A pdb=" N MET A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 277 removed outlier: 4.036A pdb=" N GLN A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.540A pdb=" N ALA A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 301 through 333 removed outlier: 3.555A pdb=" N PHE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 4.067A pdb=" N PHE A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 365 removed outlier: 3.550A pdb=" N LYS A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 398 removed outlier: 4.650A pdb=" N GLN A 379 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 409 through 437 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.857A pdb=" N HIS B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 62 through 65 removed outlier: 4.023A pdb=" N LYS B 65 " --> pdb=" O ASP B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.836A pdb=" N TYR B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 8 removed outlier: 3.717A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 68 " --> pdb=" O GLN C 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.591A pdb=" N LEU B 18 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.075A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) 272 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: 0.73 Time building geometry restraints manager: 0.54 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: 1530 1.34 - 1.46: 1003 1.46 - 1.58: 2361 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4942 Sorted by residual: bond pdb=" CB ASP A 247 " pdb=" CG ASP A 247 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.06e-01 bond pdb=" CA GLU B 44 " pdb=" CB GLU B 44 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.51e-02 4.39e+03 8.04e-01 bond pdb=" SD MET A 80 " pdb=" CE MET A 80 " ideal model delta sigma weight residual 1.791 1.769 0.022 2.50e-02 1.60e+03 7.98e-01 bond pdb=" CB THR A 61 " pdb=" CG2 THR A 61 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.52e-01 bond pdb=" CB GLU B 44 " pdb=" CG GLU B 44 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.49e-01 ... (remaining 4937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 6649 2.38 - 4.76: 61 4.76 - 7.13: 9 7.13 - 9.51: 1 9.51 - 11.89: 1 Bond angle restraints: 6721 Sorted by residual: angle pdb=" CA LEU C 103 " pdb=" CB LEU C 103 " pdb=" CG LEU C 103 " ideal model delta sigma weight residual 116.30 128.19 -11.89 3.50e+00 8.16e-02 1.15e+01 angle pdb=" C THR A 130 " pdb=" N PHE A 131 " pdb=" CA PHE A 131 " ideal model delta sigma weight residual 121.14 115.44 5.70 1.75e+00 3.27e-01 1.06e+01 angle pdb=" N ASP A 247 " pdb=" CA ASP A 247 " pdb=" C ASP A 247 " ideal model delta sigma weight residual 112.25 108.54 3.71 1.36e+00 5.41e-01 7.44e+00 angle pdb=" CA GLU B 44 " pdb=" CB GLU B 44 " pdb=" CG GLU B 44 " ideal model delta sigma weight residual 114.10 119.48 -5.38 2.00e+00 2.50e-01 7.24e+00 angle pdb=" CA LEU C 47 " pdb=" CB LEU C 47 " pdb=" CG LEU C 47 " ideal model delta sigma weight residual 116.30 124.49 -8.19 3.50e+00 8.16e-02 5.48e+00 ... (remaining 6716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 2578 16.06 - 32.11: 243 32.11 - 48.17: 59 48.17 - 64.23: 6 64.23 - 80.29: 3 Dihedral angle restraints: 2889 sinusoidal: 1068 harmonic: 1821 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual 93.00 173.29 -80.29 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CA ASP B 80 " pdb=" C ASP B 80 " pdb=" N LEU B 81 " pdb=" CA LEU B 81 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA VAL C 28 " pdb=" C VAL C 28 " pdb=" N PHE C 29 " pdb=" CA PHE C 29 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 2886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 482 0.034 - 0.068: 224 0.068 - 0.101: 68 0.101 - 0.135: 19 0.135 - 0.169: 2 Chirality restraints: 795 Sorted by residual: chirality pdb=" CA PHE A 131 " pdb=" N PHE A 131 " pdb=" C PHE A 131 " pdb=" CB PHE A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA PRO A 228 " pdb=" N PRO A 228 " pdb=" C PRO A 228 " pdb=" CB PRO A 228 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE A 366 " pdb=" N ILE A 366 " pdb=" C ILE A 366 " pdb=" CB ILE A 366 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 792 not shown) Planarity restraints: 837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 247 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" CG ASP A 247 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP A 247 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 247 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 247 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C ASP A 247 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP A 247 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A 248 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 312 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C ALA A 312 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA A 312 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 313 " 0.010 2.00e-02 2.50e+03 ... (remaining 834 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1141 2.79 - 3.32: 4636 3.32 - 3.84: 8078 3.84 - 4.37: 9062 4.37 - 4.90: 16067 Nonbonded interactions: 38984 Sorted by model distance: nonbonded pdb=" O MET A 94 " pdb=" OG1 THR A 98 " model vdw 2.259 3.040 nonbonded pdb=" O GLU A 133 " pdb=" OG SER A 314 " model vdw 2.263 3.040 nonbonded pdb=" ND2 ASN A 126 " pdb=" OG1 THR A 325 " model vdw 2.280 3.120 nonbonded pdb=" O PHE A 71 " pdb=" OG SER A 202 " model vdw 2.303 3.040 nonbonded pdb=" O LYS A 100 " pdb=" NE2 GLN A 235 " model vdw 2.322 3.120 ... (remaining 38979 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: 0.510 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.930 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.003 0.036 4944 Z= 0.130 Angle : 0.600 11.890 6725 Z= 0.310 Chirality : 0.043 0.169 795 Planarity : 0.005 0.040 837 Dihedral : 12.907 76.043 1717 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.34), residues: 633 helix: 0.40 (0.31), residues: 308 sheet: -1.43 (0.64), residues: 84 loop : -1.77 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 52 TYR 0.016 0.001 TYR A 185 PHE 0.020 0.001 PHE A 131 TRP 0.012 0.001 TRP B 53 HIS 0.001 0.000 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4942) covalent geometry : angle 0.59994 ( 6721) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.79026 ( 4) hydrogen bonds : bond 0.17893 ( 272) hydrogen bonds : angle 7.21635 ( 786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.161 Fit side-chains REVERT: A 191 MET cc_start: 0.7990 (ttp) cc_final: 0.7788 (ttp) REVERT: A 247 ASP cc_start: 0.7922 (t0) cc_final: 0.7675 (t0) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0592 time to fit residues: 4.4170 Evaluate side-chains 49 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.154015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.122186 restraints weight = 5061.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.123606 restraints weight = 4303.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.124226 restraints weight = 3680.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.124379 restraints weight = 3441.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.124692 restraints weight = 3474.922| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4944 Z= 0.163 Angle : 0.613 10.244 6725 Z= 0.318 Chirality : 0.044 0.185 795 Planarity : 0.005 0.037 837 Dihedral : 4.293 20.206 686 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.39 % Allowed : 6.57 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.34), residues: 633 helix: 1.06 (0.30), residues: 315 sheet: -1.39 (0.67), residues: 77 loop : -2.00 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 52 TYR 0.012 0.001 TYR A 185 PHE 0.038 0.002 PHE A 131 TRP 0.008 0.001 TRP A 267 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4942) covalent geometry : angle 0.61224 ( 6721) SS BOND : bond 0.00453 ( 2) SS BOND : angle 1.12057 ( 4) hydrogen bonds : bond 0.04485 ( 272) hydrogen bonds : angle 4.80476 ( 786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.175 Fit side-chains REVERT: A 247 ASP cc_start: 0.8346 (t0) cc_final: 0.8106 (t0) REVERT: A 375 MET cc_start: 0.8378 (mtm) cc_final: 0.8089 (mtp) REVERT: B 39 GLN cc_start: 0.8387 (tt0) cc_final: 0.8156 (tt0) outliers start: 7 outliers final: 6 residues processed: 55 average time/residue: 0.0757 time to fit residues: 5.5046 Evaluate side-chains 55 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.152373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120530 restraints weight = 5012.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.121248 restraints weight = 4453.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121646 restraints weight = 4040.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.121884 restraints weight = 3840.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122110 restraints weight = 3697.395| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4944 Z= 0.151 Angle : 0.573 7.745 6725 Z= 0.301 Chirality : 0.043 0.181 795 Planarity : 0.004 0.038 837 Dihedral : 4.263 20.204 686 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 1.59 % Allowed : 13.35 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.34), residues: 633 helix: 1.25 (0.30), residues: 315 sheet: -1.47 (0.65), residues: 77 loop : -2.02 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.009 0.001 TYR A 185 PHE 0.036 0.002 PHE C 50 TRP 0.008 0.001 TRP A 229 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 4942) covalent geometry : angle 0.57301 ( 6721) SS BOND : bond 0.00461 ( 2) SS BOND : angle 0.77872 ( 4) hydrogen bonds : bond 0.04193 ( 272) hydrogen bonds : angle 4.53229 ( 786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.103 Fit side-chains REVERT: A 247 ASP cc_start: 0.8407 (t0) cc_final: 0.8070 (t0) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.0483 time to fit residues: 3.4676 Evaluate side-chains 57 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 42 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.151175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.119442 restraints weight = 5040.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.120497 restraints weight = 4408.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120834 restraints weight = 3975.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120898 restraints weight = 3791.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.120978 restraints weight = 3802.973| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4944 Z= 0.153 Angle : 0.569 6.859 6725 Z= 0.299 Chirality : 0.043 0.178 795 Planarity : 0.004 0.038 837 Dihedral : 4.250 20.678 686 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.59 % Allowed : 14.54 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.35), residues: 633 helix: 1.32 (0.30), residues: 315 sheet: -1.51 (0.66), residues: 77 loop : -2.02 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 19 TYR 0.008 0.001 TYR A 168 PHE 0.033 0.002 PHE A 131 TRP 0.008 0.001 TRP A 267 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4942) covalent geometry : angle 0.56935 ( 6721) SS BOND : bond 0.00452 ( 2) SS BOND : angle 0.72308 ( 4) hydrogen bonds : bond 0.04075 ( 272) hydrogen bonds : angle 4.37410 ( 786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.173 Fit side-chains REVERT: A 80 MET cc_start: 0.7742 (ttm) cc_final: 0.7511 (ttm) REVERT: A 247 ASP cc_start: 0.8392 (t0) cc_final: 0.7936 (t0) outliers start: 13 outliers final: 8 residues processed: 58 average time/residue: 0.0561 time to fit residues: 4.5212 Evaluate side-chains 57 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.152802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.120910 restraints weight = 5069.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121970 restraints weight = 4284.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121970 restraints weight = 3851.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121970 restraints weight = 3851.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121970 restraints weight = 3851.943| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4944 Z= 0.133 Angle : 0.552 6.092 6725 Z= 0.289 Chirality : 0.042 0.172 795 Planarity : 0.004 0.039 837 Dihedral : 4.225 20.194 686 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.99 % Allowed : 17.13 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.34), residues: 633 helix: 1.42 (0.30), residues: 315 sheet: -1.05 (0.70), residues: 69 loop : -2.12 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 19 TYR 0.009 0.001 TYR A 168 PHE 0.036 0.001 PHE A 131 TRP 0.007 0.001 TRP A 229 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4942) covalent geometry : angle 0.55164 ( 6721) SS BOND : bond 0.00338 ( 2) SS BOND : angle 0.61521 ( 4) hydrogen bonds : bond 0.03888 ( 272) hydrogen bonds : angle 4.27845 ( 786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.178 Fit side-chains REVERT: A 80 MET cc_start: 0.7698 (ttm) cc_final: 0.7448 (ttm) REVERT: A 247 ASP cc_start: 0.8448 (t0) cc_final: 0.7954 (t0) outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 0.0731 time to fit residues: 5.5263 Evaluate side-chains 57 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 17 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.152270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.119379 restraints weight = 5115.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120974 restraints weight = 4295.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.121522 restraints weight = 3721.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.123134 restraints weight = 3499.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.122815 restraints weight = 3187.291| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4944 Z= 0.139 Angle : 0.548 6.104 6725 Z= 0.289 Chirality : 0.043 0.177 795 Planarity : 0.004 0.038 837 Dihedral : 4.181 20.443 686 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.39 % Allowed : 17.73 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.34), residues: 633 helix: 1.47 (0.30), residues: 315 sheet: -1.08 (0.70), residues: 69 loop : -2.13 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 19 TYR 0.010 0.001 TYR C 37 PHE 0.033 0.001 PHE A 131 TRP 0.007 0.001 TRP A 229 HIS 0.000 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4942) covalent geometry : angle 0.54796 ( 6721) SS BOND : bond 0.00393 ( 2) SS BOND : angle 0.62274 ( 4) hydrogen bonds : bond 0.03905 ( 272) hydrogen bonds : angle 4.23295 ( 786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.109 Fit side-chains REVERT: A 80 MET cc_start: 0.7755 (ttm) cc_final: 0.7525 (ttm) REVERT: A 247 ASP cc_start: 0.8397 (t0) cc_final: 0.7887 (t0) REVERT: A 327 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7557 (m-10) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.0680 time to fit residues: 5.5017 Evaluate side-chains 62 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 39 optimal weight: 0.5980 chunk 44 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 17 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.154470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.122160 restraints weight = 5026.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.123747 restraints weight = 4217.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.125416 restraints weight = 3681.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.125503 restraints weight = 3264.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.125653 restraints weight = 3222.243| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4944 Z= 0.119 Angle : 0.533 5.575 6725 Z= 0.281 Chirality : 0.042 0.173 795 Planarity : 0.004 0.038 837 Dihedral : 4.143 19.609 686 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.99 % Allowed : 18.53 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.35), residues: 633 helix: 1.64 (0.30), residues: 312 sheet: -1.03 (0.70), residues: 69 loop : -2.18 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.008 0.001 TYR A 168 PHE 0.036 0.001 PHE C 50 TRP 0.007 0.001 TRP A 229 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4942) covalent geometry : angle 0.53347 ( 6721) SS BOND : bond 0.00251 ( 2) SS BOND : angle 0.49017 ( 4) hydrogen bonds : bond 0.03727 ( 272) hydrogen bonds : angle 4.17436 ( 786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.174 Fit side-chains REVERT: A 80 MET cc_start: 0.7750 (ttm) cc_final: 0.7503 (ttm) REVERT: A 247 ASP cc_start: 0.8327 (t0) cc_final: 0.7796 (t0) REVERT: A 327 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7535 (m-10) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.0670 time to fit residues: 5.3837 Evaluate side-chains 59 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 37 optimal weight: 0.0570 chunk 46 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.0370 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.154402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.122124 restraints weight = 5108.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.123582 restraints weight = 4339.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.124014 restraints weight = 3791.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.124014 restraints weight = 3577.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.124014 restraints weight = 3577.194| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4944 Z= 0.122 Angle : 0.557 9.294 6725 Z= 0.286 Chirality : 0.042 0.174 795 Planarity : 0.004 0.037 837 Dihedral : 4.089 18.931 686 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.99 % Allowed : 17.73 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.35), residues: 633 helix: 1.64 (0.30), residues: 312 sheet: -0.98 (0.71), residues: 69 loop : -2.17 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 19 TYR 0.009 0.001 TYR C 37 PHE 0.033 0.001 PHE C 50 TRP 0.007 0.001 TRP A 229 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4942) covalent geometry : angle 0.55726 ( 6721) SS BOND : bond 0.00294 ( 2) SS BOND : angle 0.52701 ( 4) hydrogen bonds : bond 0.03702 ( 272) hydrogen bonds : angle 4.17602 ( 786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.104 Fit side-chains REVERT: A 80 MET cc_start: 0.7757 (ttm) cc_final: 0.7520 (ttm) REVERT: A 247 ASP cc_start: 0.8363 (t0) cc_final: 0.7828 (t0) REVERT: A 327 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7633 (m-10) outliers start: 15 outliers final: 11 residues processed: 64 average time/residue: 0.0504 time to fit residues: 4.3820 Evaluate side-chains 64 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 13 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.0770 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.155351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.122642 restraints weight = 5000.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.123932 restraints weight = 4106.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124985 restraints weight = 3622.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.125044 restraints weight = 3311.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.125154 restraints weight = 3276.705| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4944 Z= 0.122 Angle : 0.595 15.591 6725 Z= 0.295 Chirality : 0.042 0.174 795 Planarity : 0.004 0.036 837 Dihedral : 4.096 18.844 686 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.19 % Allowed : 17.33 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.34), residues: 633 helix: 1.48 (0.30), residues: 319 sheet: -0.97 (0.71), residues: 69 loop : -2.35 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.007 0.001 TYR C 37 PHE 0.033 0.001 PHE A 131 TRP 0.007 0.001 TRP A 229 HIS 0.001 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4942) covalent geometry : angle 0.59521 ( 6721) SS BOND : bond 0.00253 ( 2) SS BOND : angle 0.50423 ( 4) hydrogen bonds : bond 0.03721 ( 272) hydrogen bonds : angle 4.16690 ( 786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.168 Fit side-chains REVERT: A 80 MET cc_start: 0.7700 (ttm) cc_final: 0.7473 (ttm) REVERT: A 247 ASP cc_start: 0.8382 (t0) cc_final: 0.7855 (t0) REVERT: A 327 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7609 (m-10) REVERT: A 371 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7875 (mt) outliers start: 16 outliers final: 12 residues processed: 65 average time/residue: 0.0398 time to fit residues: 3.5765 Evaluate side-chains 67 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 61 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 0.0370 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 210 ASN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.156314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.124189 restraints weight = 5034.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125667 restraints weight = 4277.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.126018 restraints weight = 3775.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.126538 restraints weight = 3588.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126741 restraints weight = 3420.422| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4944 Z= 0.122 Angle : 0.587 14.275 6725 Z= 0.295 Chirality : 0.042 0.170 795 Planarity : 0.004 0.036 837 Dihedral : 4.058 18.446 686 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.19 % Allowed : 17.93 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.35), residues: 633 helix: 1.54 (0.30), residues: 319 sheet: -0.92 (0.71), residues: 69 loop : -2.25 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.006 0.001 TYR A 168 PHE 0.033 0.001 PHE A 131 TRP 0.005 0.001 TRP A 229 HIS 0.000 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4942) covalent geometry : angle 0.58690 ( 6721) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.48849 ( 4) hydrogen bonds : bond 0.03665 ( 272) hydrogen bonds : angle 4.13722 ( 786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.175 Fit side-chains REVERT: A 80 MET cc_start: 0.7706 (ttm) cc_final: 0.7472 (ttm) REVERT: A 247 ASP cc_start: 0.8340 (t0) cc_final: 0.7830 (t0) REVERT: A 327 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7679 (m-10) REVERT: A 371 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7814 (mt) outliers start: 16 outliers final: 12 residues processed: 64 average time/residue: 0.0674 time to fit residues: 5.8457 Evaluate side-chains 67 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 60 optimal weight: 3.9990 chunk 52 optimal weight: 0.0470 chunk 14 optimal weight: 0.0010 chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 22 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 49 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN C 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.159424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.127460 restraints weight = 5038.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.129083 restraints weight = 4177.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.130347 restraints weight = 3643.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.130681 restraints weight = 3269.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.130789 restraints weight = 3197.352| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4944 Z= 0.114 Angle : 0.578 14.256 6725 Z= 0.293 Chirality : 0.042 0.167 795 Planarity : 0.004 0.036 837 Dihedral : 4.041 17.670 686 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.19 % Allowed : 18.73 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.35), residues: 633 helix: 1.58 (0.30), residues: 319 sheet: -0.94 (0.70), residues: 74 loop : -2.23 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.007 0.001 TYR C 59 PHE 0.034 0.001 PHE A 131 TRP 0.007 0.001 TRP A 229 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4942) covalent geometry : angle 0.57858 ( 6721) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.36622 ( 4) hydrogen bonds : bond 0.03541 ( 272) hydrogen bonds : angle 4.09688 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 950.07 seconds wall clock time: 17 minutes 6.16 seconds (1026.16 seconds total)