Starting phenix.real_space_refine on Tue Aug 4 14:53:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ove_70899/08_2026/9ove_70899.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ove_70899/08_2026/9ove_70899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ove_70899/08_2026/9ove_70899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ove_70899/08_2026/9ove_70899.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ove_70899/08_2026/9ove_70899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ove_70899/08_2026/9ove_70899.map" } resolution = 4.1 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 16 5.16 5 C 2674 2.51 5 N 661 2.21 5 O 685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 4039 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2014 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 15, 'TRANS': 249} Chain breaks: 1 Chain: "A" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2022 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.16, per 1000 atoms: 0.29 Number of scatterers: 4039 At special positions: 0 Unit cell: (69.66, 81.7, 100.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 16 16.00 O 685 8.00 N 661 7.00 C 2674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS A 53 " 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: 0.34 Conformation dependent library (CDL) restraints added in 158.5 milliseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 990 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'B' and resid 4 through 51 removed outlier: 4.414A pdb=" N ALA B 8 " --> pdb=" O GLY B 4 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 4.053A pdb=" N ALA B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 68 Processing helix chain 'B' and resid 70 through 79 removed outlier: 3.588A pdb=" N ARG B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 116 through 152 Proline residue: B 132 - end of helix removed outlier: 3.858A pdb=" N VAL B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 185 removed outlier: 3.835A pdb=" N PHE B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 202 through 213 Processing helix chain 'B' and resid 230 through 264 removed outlier: 3.727A pdb=" N HIS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 270 Processing helix chain 'A' and resid 6 through 29 Processing helix chain 'A' and resid 30 through 51 removed outlier: 4.232A pdb=" N ALA A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 4.177A pdb=" N LEU A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 3.945A pdb=" N VAL A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 116 through 151 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 167 through 196 Proline residue: A 188 - end of helix removed outlier: 3.901A pdb=" N LEU A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 213 removed outlier: 3.574A pdb=" N LEU A 212 " --> pdb=" O CYS A 208 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 263 removed outlier: 3.706A pdb=" N HIS A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 305 hydrogen bonds defined for protein. 915 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: 0.53 Time building geometry restraints manager: 0.45 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: 1250 1.34 - 1.46: 953 1.46 - 1.58: 1919 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4144 Sorted by residual: bond pdb=" C ALA A 56 " pdb=" N PRO A 57 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.07e-01 bond pdb=" C VAL B 131 " pdb=" N PRO B 132 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.36e-02 5.41e+03 3.45e-01 bond pdb=" CA VAL A 131 " pdb=" C VAL A 131 " ideal model delta sigma weight residual 1.524 1.531 -0.007 1.11e-02 8.12e+03 3.44e-01 bond pdb=" C ALA B 56 " pdb=" N PRO B 57 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.28e-02 6.10e+03 3.16e-01 bond pdb=" CA GLY B 30 " pdb=" C GLY B 30 " ideal model delta sigma weight residual 1.515 1.523 -0.008 1.43e-02 4.89e+03 3.13e-01 ... (remaining 4139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 5542 1.46 - 2.92: 105 2.92 - 4.38: 16 4.38 - 5.83: 13 5.83 - 7.29: 6 Bond angle restraints: 5682 Sorted by residual: angle pdb=" CA LEU B 251 " pdb=" CB LEU B 251 " pdb=" CG LEU B 251 " ideal model delta sigma weight residual 116.30 123.59 -7.29 3.50e+00 8.16e-02 4.34e+00 angle pdb=" N GLY B 30 " pdb=" CA GLY B 30 " pdb=" C GLY B 30 " ideal model delta sigma weight residual 112.34 116.34 -4.00 2.04e+00 2.40e-01 3.85e+00 angle pdb=" CA LEU A 18 " pdb=" CB LEU A 18 " pdb=" CG LEU A 18 " ideal model delta sigma weight residual 116.30 122.92 -6.62 3.50e+00 8.16e-02 3.57e+00 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 110.80 114.62 -3.82 2.13e+00 2.20e-01 3.22e+00 angle pdb=" CA LEU A 177 " pdb=" CB LEU A 177 " pdb=" CG LEU A 177 " ideal model delta sigma weight residual 116.30 122.33 -6.03 3.50e+00 8.16e-02 2.96e+00 ... (remaining 5677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.55: 2115 11.55 - 23.11: 166 23.11 - 34.66: 82 34.66 - 46.21: 31 46.21 - 57.77: 2 Dihedral angle restraints: 2396 sinusoidal: 861 harmonic: 1535 Sorted by residual: dihedral pdb=" CA LEU B 271 " pdb=" C LEU B 271 " pdb=" N PRO B 272 " pdb=" CA PRO B 272 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" N LEU B 145 " pdb=" CA LEU B 145 " pdb=" CB LEU B 145 " pdb=" CG LEU B 145 " ideal model delta sinusoidal sigma weight residual -60.00 -110.83 50.83 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA ALA B 56 " pdb=" C ALA B 56 " pdb=" N PRO B 57 " pdb=" CA PRO B 57 " ideal model delta harmonic sigma weight residual -180.00 -165.17 -14.83 0 5.00e+00 4.00e-02 8.80e+00 ... (remaining 2393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 449 0.026 - 0.052: 151 0.052 - 0.077: 66 0.077 - 0.103: 19 0.103 - 0.129: 6 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA VAL B 152 " pdb=" N VAL B 152 " pdb=" C VAL B 152 " pdb=" CB VAL B 152 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA PRO A 57 " pdb=" N PRO A 57 " pdb=" C PRO A 57 " pdb=" CB PRO A 57 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA PRO A 31 " pdb=" N PRO A 31 " pdb=" C PRO A 31 " pdb=" CB PRO A 31 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.95e-01 ... (remaining 688 not shown) Planarity restraints: 697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 164 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 165 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 273 " 0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO A 274 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 183 " 0.005 2.00e-02 2.50e+03 9.95e-03 9.90e-01 pdb=" C VAL A 183 " -0.017 2.00e-02 2.50e+03 pdb=" O VAL A 183 " 0.006 2.00e-02 2.50e+03 pdb=" N CYS A 184 " 0.006 2.00e-02 2.50e+03 ... (remaining 694 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.10: 3112 3.10 - 3.61: 5551 3.61 - 4.12: 6081 4.12 - 4.63: 9847 4.63 - 5.14: 11681 Nonbonded interactions: 36272 Sorted by model distance: nonbonded pdb=" N THR B 105 " pdb=" OG1 THR B 105 " model vdw 2.594 2.496 nonbonded pdb=" O ILE A 215 " pdb=" K K A 302 " model vdw 2.601 2.850 nonbonded pdb=" C THR B 133 " pdb=" OG1 THR B 133 " model vdw 2.614 2.616 nonbonded pdb=" O ILE B 215 " pdb=" K K A 302 " model vdw 2.621 2.850 nonbonded pdb=" O GLY B 216 " pdb=" K K A 302 " model vdw 2.622 2.850 ... (remaining 36267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 81 or resid 89 through 301)) selection = chain 'B' } 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.850 Find NCS groups from input model: 0.040 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 0.019 4145 Z= 0.102 Angle : 0.561 7.293 5684 Z= 0.259 Chirality : 0.033 0.129 691 Planarity : 0.004 0.035 697 Dihedral : 11.478 57.766 1403 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.06 % Favored : 96.75 % Rotamer: Outliers : 3.39 % Allowed : 9.69 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.39), residues: 523 helix: 2.65 (0.26), residues: 395 sheet: None (None), residues: 0 loop : -1.35 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 71 TYR 0.010 0.001 TYR A 17 PHE 0.013 0.001 PHE A 126 TRP 0.006 0.001 TRP B 156 HIS 0.002 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.10 ( 4144) covalent geometry : angle 0.56096 / 0.26 ( 5682) SS BOND : bond 0.00031 / 0.02 ( 1) SS BOND : angle 0.19213 / 0.09 ( 2) hydrogen bonds : bond 0.09660 / 7.02 ( 305) hydrogen bonds : angle 3.93498 / 3.02 ( 915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 GLU cc_start: 0.9609 (pp20) cc_final: 0.9080 (pp20) REVERT: B 79 ASN cc_start: 0.8350 (t0) cc_final: 0.7876 (m110) REVERT: B 115 LEU cc_start: 0.8845 (pt) cc_final: 0.8515 (mp) REVERT: B 126 PHE cc_start: 0.9034 (t80) cc_final: 0.8775 (t80) REVERT: B 185 PHE cc_start: 0.9099 (m-10) cc_final: 0.8844 (m-10) REVERT: B 203 ASP cc_start: 0.8135 (m-30) cc_final: 0.7879 (m-30) REVERT: A 47 LEU cc_start: 0.9287 (tp) cc_final: 0.9077 (tp) REVERT: A 210 ILE cc_start: 0.9112 (tp) cc_final: 0.8889 (tp) REVERT: A 215 ILE cc_start: 0.7285 (mm) cc_final: 0.7035 (mm) REVERT: A 220 TYR cc_start: 0.9391 (m-80) cc_final: 0.8953 (m-80) outliers start: 14 outliers final: 1 residues processed: 179 average time/residue: 0.0652 time to fit residues: 14.6169 Evaluate side-chains 132 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.0020 chunk 25 optimal weight: 0.0670 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 GLN B 228 GLN B 263 HIS A 172 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.111000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095876 restraints weight = 14401.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.098034 restraints weight = 9227.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.100007 restraints weight = 6731.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100946 restraints weight = 5029.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.101948 restraints weight = 4160.515| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4145 Z= 0.124 Angle : 0.651 8.747 5684 Z= 0.302 Chirality : 0.037 0.138 691 Planarity : 0.005 0.053 697 Dihedral : 3.649 16.258 571 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.02 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.39), residues: 523 helix: 2.49 (0.26), residues: 402 sheet: None (None), residues: 0 loop : -1.13 (0.63), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 166 TYR 0.019 0.001 TYR B 234 PHE 0.013 0.001 PHE A 126 TRP 0.007 0.001 TRP B 163 HIS 0.007 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 4144) covalent geometry : angle 0.64968 / 0.30 ( 5682) SS BOND : bond 0.00068 / 0.04 ( 1) SS BOND : angle 2.04032 / 0.94 ( 2) hydrogen bonds : bond 0.03883 / 2.63 ( 305) hydrogen bonds : angle 3.54615 / 2.64 ( 915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 GLU cc_start: 0.9559 (pp20) cc_final: 0.9036 (pp20) REVERT: B 39 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8771 (tm-30) REVERT: B 104 ILE cc_start: 0.9244 (tp) cc_final: 0.9035 (tp) REVERT: B 115 LEU cc_start: 0.8564 (pt) cc_final: 0.8301 (mp) REVERT: B 203 ASP cc_start: 0.8427 (m-30) cc_final: 0.7414 (m-30) REVERT: A 74 ARG cc_start: 0.8000 (ptt180) cc_final: 0.7744 (ptp90) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.0571 time to fit residues: 11.5589 Evaluate side-chains 126 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.105109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090966 restraints weight = 14915.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093198 restraints weight = 9007.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094634 restraints weight = 6311.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.095972 restraints weight = 4860.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096880 restraints weight = 3862.465| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4145 Z= 0.169 Angle : 0.669 6.644 5684 Z= 0.330 Chirality : 0.038 0.157 691 Planarity : 0.005 0.046 697 Dihedral : 3.966 18.160 571 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.59 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.38), residues: 523 helix: 2.22 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -1.29 (0.61), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 166 TYR 0.030 0.002 TYR B 234 PHE 0.011 0.001 PHE B 122 TRP 0.011 0.001 TRP A 161 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 4144) covalent geometry : angle 0.66864 / 0.33 ( 5682) SS BOND : bond 0.00127 / 0.08 ( 1) SS BOND : angle 1.75366 / 0.83 ( 2) hydrogen bonds : bond 0.04392 / 2.94 ( 305) hydrogen bonds : angle 3.65305 / 2.76 ( 915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 TYR cc_start: 0.8396 (t80) cc_final: 0.8168 (t80) REVERT: B 33 GLU cc_start: 0.9550 (pp20) cc_final: 0.9222 (pp20) REVERT: B 39 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8862 (tm-30) REVERT: B 46 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8975 (tm-30) REVERT: B 49 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8476 (pp30) REVERT: B 104 ILE cc_start: 0.9264 (tp) cc_final: 0.9020 (tp) REVERT: B 111 TYR cc_start: 0.8088 (t80) cc_final: 0.7843 (t80) REVERT: B 185 PHE cc_start: 0.9179 (m-10) cc_final: 0.8931 (m-10) REVERT: B 203 ASP cc_start: 0.8541 (m-30) cc_final: 0.7683 (m-30) REVERT: A 64 GLU cc_start: 0.9369 (tm-30) cc_final: 0.9156 (tm-30) REVERT: A 74 ARG cc_start: 0.8106 (ptt180) cc_final: 0.7819 (ptp90) REVERT: A 194 HIS cc_start: 0.7841 (t-90) cc_final: 0.7640 (t-170) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0607 time to fit residues: 11.4904 Evaluate side-chains 118 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.107408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.091938 restraints weight = 14811.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.094400 restraints weight = 9271.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095958 restraints weight = 6566.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.097458 restraints weight = 5081.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.098240 restraints weight = 4103.292| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4145 Z= 0.123 Angle : 0.639 7.844 5684 Z= 0.301 Chirality : 0.036 0.120 691 Planarity : 0.004 0.040 697 Dihedral : 3.815 16.454 571 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.38), residues: 523 helix: 2.33 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -1.22 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 50 TYR 0.007 0.001 TYR B 234 PHE 0.013 0.001 PHE A 126 TRP 0.006 0.001 TRP B 161 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 4144) covalent geometry : angle 0.63847 / 0.30 ( 5682) SS BOND : bond 0.00062 / 0.04 ( 1) SS BOND : angle 0.88427 / 0.42 ( 2) hydrogen bonds : bond 0.04010 / 2.68 ( 305) hydrogen bonds : angle 3.57319 / 2.68 ( 915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 33 GLU cc_start: 0.9572 (pp20) cc_final: 0.9269 (pp20) REVERT: B 39 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8798 (tm-30) REVERT: B 104 ILE cc_start: 0.9250 (tp) cc_final: 0.9010 (tp) REVERT: B 185 PHE cc_start: 0.9193 (m-10) cc_final: 0.8873 (m-10) REVERT: B 203 ASP cc_start: 0.8536 (m-30) cc_final: 0.7568 (m-30) REVERT: A 194 HIS cc_start: 0.8037 (t-90) cc_final: 0.7792 (t-170) REVERT: A 261 ASP cc_start: 0.8905 (m-30) cc_final: 0.8664 (m-30) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0553 time to fit residues: 10.4870 Evaluate side-chains 124 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.106562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.092060 restraints weight = 14707.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094320 restraints weight = 9186.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095656 restraints weight = 6470.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096497 restraints weight = 5045.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097606 restraints weight = 4290.756| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4145 Z= 0.145 Angle : 0.659 7.051 5684 Z= 0.319 Chirality : 0.037 0.123 691 Planarity : 0.005 0.057 697 Dihedral : 3.912 16.352 571 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.97 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.38), residues: 523 helix: 2.19 (0.26), residues: 401 sheet: None (None), residues: 0 loop : -1.27 (0.63), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 50 TYR 0.028 0.002 TYR B 234 PHE 0.012 0.001 PHE A 126 TRP 0.027 0.002 TRP A 156 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 4144) covalent geometry : angle 0.65854 / 0.32 ( 5682) SS BOND : bond 0.00004 / 0.00 ( 1) SS BOND : angle 0.76321 / 0.36 ( 2) hydrogen bonds : bond 0.04190 / 2.78 ( 305) hydrogen bonds : angle 3.61115 / 2.69 ( 915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 33 GLU cc_start: 0.9545 (pp20) cc_final: 0.8827 (pp20) REVERT: B 39 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8837 (tm-30) REVERT: B 104 ILE cc_start: 0.9274 (tp) cc_final: 0.9031 (tp) REVERT: B 111 TYR cc_start: 0.8228 (t80) cc_final: 0.7968 (t80) REVERT: B 185 PHE cc_start: 0.9172 (m-10) cc_final: 0.8866 (m-10) REVERT: B 203 ASP cc_start: 0.8588 (m-30) cc_final: 0.7622 (m-30) REVERT: A 74 ARG cc_start: 0.8127 (ptp90) cc_final: 0.7917 (ptp90) REVERT: A 194 HIS cc_start: 0.7998 (t-90) cc_final: 0.7750 (t-170) REVERT: A 261 ASP cc_start: 0.8888 (m-30) cc_final: 0.8639 (m-30) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0569 time to fit residues: 10.6045 Evaluate side-chains 121 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 0.0010 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.108779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.094725 restraints weight = 14533.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096856 restraints weight = 8967.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098699 restraints weight = 6393.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.099515 restraints weight = 4776.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.100594 restraints weight = 3935.878| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4145 Z= 0.120 Angle : 0.657 7.511 5684 Z= 0.305 Chirality : 0.037 0.126 691 Planarity : 0.005 0.039 697 Dihedral : 3.863 16.151 571 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.39), residues: 523 helix: 2.28 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -1.39 (0.62), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.017 0.001 TYR B 206 PHE 0.013 0.001 PHE A 126 TRP 0.012 0.001 TRP B 163 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 4144) covalent geometry : angle 0.65699 / 0.30 ( 5682) SS BOND : bond 0.00069 / 0.04 ( 1) SS BOND : angle 0.57623 / 0.27 ( 2) hydrogen bonds : bond 0.03906 / 2.58 ( 305) hydrogen bonds : angle 3.50917 / 2.61 ( 915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 33 GLU cc_start: 0.9513 (pp20) cc_final: 0.9306 (pp20) REVERT: B 39 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8747 (tm-30) REVERT: B 104 ILE cc_start: 0.9244 (tp) cc_final: 0.9004 (tp) REVERT: B 126 PHE cc_start: 0.8761 (t80) cc_final: 0.8368 (t80) REVERT: B 185 PHE cc_start: 0.9143 (m-10) cc_final: 0.8859 (m-10) REVERT: B 203 ASP cc_start: 0.8444 (m-30) cc_final: 0.7359 (m-30) REVERT: B 220 TYR cc_start: 0.9517 (m-80) cc_final: 0.8428 (m-80) REVERT: A 17 TYR cc_start: 0.8660 (t80) cc_final: 0.8431 (t80) REVERT: A 194 HIS cc_start: 0.7838 (t-90) cc_final: 0.7622 (t-170) REVERT: A 261 ASP cc_start: 0.8752 (m-30) cc_final: 0.8486 (m-30) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0620 time to fit residues: 11.7229 Evaluate side-chains 121 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 18 optimal weight: 0.0970 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.110129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.094815 restraints weight = 14480.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096953 restraints weight = 8991.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.098757 restraints weight = 6463.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.100104 restraints weight = 4905.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.100935 restraints weight = 3910.342| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4145 Z= 0.115 Angle : 0.655 7.294 5684 Z= 0.304 Chirality : 0.037 0.121 691 Planarity : 0.004 0.046 697 Dihedral : 3.800 16.071 571 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 2.24 (0.39), residues: 523 helix: 2.32 (0.26), residues: 400 sheet: None (None), residues: 0 loop : -1.45 (0.62), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.018 0.002 TYR B 206 PHE 0.015 0.001 PHE A 126 TRP 0.005 0.001 TRP A 161 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 4144) covalent geometry : angle 0.65553 / 0.30 ( 5682) SS BOND : bond 0.00061 / 0.04 ( 1) SS BOND : angle 0.51059 / 0.24 ( 2) hydrogen bonds : bond 0.03783 / 2.49 ( 305) hydrogen bonds : angle 3.46979 / 2.58 ( 915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8844 (tm-30) REVERT: B 104 ILE cc_start: 0.9252 (tp) cc_final: 0.8779 (tt) REVERT: B 126 PHE cc_start: 0.8834 (t80) cc_final: 0.8413 (t80) REVERT: B 185 PHE cc_start: 0.9166 (m-10) cc_final: 0.8866 (m-10) REVERT: B 203 ASP cc_start: 0.8472 (m-30) cc_final: 0.7388 (m-30) REVERT: B 220 TYR cc_start: 0.9498 (m-80) cc_final: 0.8466 (m-80) REVERT: A 17 TYR cc_start: 0.8696 (t80) cc_final: 0.8443 (t80) REVERT: A 194 HIS cc_start: 0.7926 (t-90) cc_final: 0.7704 (t-170) REVERT: A 221 VAL cc_start: 0.9582 (t) cc_final: 0.9334 (m) REVERT: A 224 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8513 (mm-30) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0540 time to fit residues: 10.3505 Evaluate side-chains 122 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 10 optimal weight: 0.0060 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 50 optimal weight: 0.2980 chunk 48 optimal weight: 0.0060 chunk 43 optimal weight: 0.8980 overall best weight: 0.1612 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.110300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.096110 restraints weight = 14204.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.098549 restraints weight = 8793.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.100065 restraints weight = 6141.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101459 restraints weight = 4711.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.102540 restraints weight = 3720.157| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4145 Z= 0.121 Angle : 0.676 7.876 5684 Z= 0.311 Chirality : 0.037 0.120 691 Planarity : 0.004 0.045 697 Dihedral : 3.760 16.178 571 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.82 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 2.12 (0.38), residues: 523 helix: 2.22 (0.26), residues: 402 sheet: None (None), residues: 0 loop : -1.54 (0.62), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 74 TYR 0.035 0.002 TYR B 234 PHE 0.010 0.001 PHE A 126 TRP 0.006 0.001 TRP A 199 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 4144) covalent geometry : angle 0.67650 / 0.31 ( 5682) SS BOND : bond 0.00069 / 0.04 ( 1) SS BOND : angle 0.44910 / 0.21 ( 2) hydrogen bonds : bond 0.03633 / 2.40 ( 305) hydrogen bonds : angle 3.43933 / 2.58 ( 915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 GLU cc_start: 0.9381 (pp20) cc_final: 0.9015 (pp20) REVERT: B 39 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8789 (tm-30) REVERT: B 104 ILE cc_start: 0.9228 (tp) cc_final: 0.9007 (tp) REVERT: B 126 PHE cc_start: 0.8829 (t80) cc_final: 0.8416 (t80) REVERT: B 185 PHE cc_start: 0.9178 (m-10) cc_final: 0.8878 (m-10) REVERT: B 203 ASP cc_start: 0.8423 (m-30) cc_final: 0.7508 (m-30) REVERT: B 220 TYR cc_start: 0.9464 (m-80) cc_final: 0.8362 (m-80) REVERT: A 17 TYR cc_start: 0.8648 (t80) cc_final: 0.8425 (t80) REVERT: A 43 LEU cc_start: 0.9413 (tt) cc_final: 0.9013 (tt) REVERT: A 46 GLN cc_start: 0.9058 (pp30) cc_final: 0.8573 (pp30) REVERT: A 122 PHE cc_start: 0.8908 (t80) cc_final: 0.8618 (t80) REVERT: A 147 LEU cc_start: 0.9328 (tt) cc_final: 0.9121 (pp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0506 time to fit residues: 9.4110 Evaluate side-chains 119 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.108119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.093760 restraints weight = 14652.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.095860 restraints weight = 9092.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.097656 restraints weight = 6541.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098959 restraints weight = 5011.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.099621 restraints weight = 3934.329| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4145 Z= 0.121 Angle : 0.683 8.050 5684 Z= 0.316 Chirality : 0.037 0.118 691 Planarity : 0.005 0.043 697 Dihedral : 3.832 16.839 571 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.38), residues: 523 helix: 2.23 (0.26), residues: 403 sheet: None (None), residues: 0 loop : -1.47 (0.63), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 166 TYR 0.018 0.002 TYR A 241 PHE 0.013 0.001 PHE A 126 TRP 0.026 0.001 TRP B 199 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4144) covalent geometry : angle 0.68314 / 0.32 ( 5682) SS BOND : bond 0.00013 / 0.01 ( 1) SS BOND : angle 0.58033 / 0.28 ( 2) hydrogen bonds : bond 0.03600 / 2.38 ( 305) hydrogen bonds : angle 3.42780 / 2.56 ( 915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 GLU cc_start: 0.9379 (pp20) cc_final: 0.8999 (pp20) REVERT: B 39 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8843 (tm-30) REVERT: B 104 ILE cc_start: 0.9230 (tp) cc_final: 0.9009 (tp) REVERT: B 126 PHE cc_start: 0.8883 (t80) cc_final: 0.8445 (t80) REVERT: B 185 PHE cc_start: 0.9204 (m-10) cc_final: 0.8895 (m-10) REVERT: B 203 ASP cc_start: 0.8511 (m-30) cc_final: 0.7409 (m-30) REVERT: B 220 TYR cc_start: 0.9510 (m-80) cc_final: 0.8571 (m-80) REVERT: A 17 TYR cc_start: 0.8716 (t80) cc_final: 0.8444 (t80) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.0520 time to fit residues: 9.4963 Evaluate side-chains 121 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.0270 chunk 51 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.106709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.091796 restraints weight = 14893.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094033 restraints weight = 9232.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.095589 restraints weight = 6521.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.096812 restraints weight = 4985.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097660 restraints weight = 4020.698| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4145 Z= 0.120 Angle : 0.698 7.900 5684 Z= 0.322 Chirality : 0.038 0.122 691 Planarity : 0.004 0.044 697 Dihedral : 3.830 15.878 571 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.40 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.39), residues: 523 helix: 2.26 (0.26), residues: 403 sheet: None (None), residues: 0 loop : -1.53 (0.62), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 166 TYR 0.017 0.001 TYR A 241 PHE 0.014 0.001 PHE A 126 TRP 0.016 0.001 TRP B 199 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 4144) covalent geometry : angle 0.69812 / 0.32 ( 5682) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 0.46392 / 0.22 ( 2) hydrogen bonds : bond 0.03669 / 2.42 ( 305) hydrogen bonds : angle 3.40289 / 2.54 ( 915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 GLU cc_start: 0.9424 (pp20) cc_final: 0.9025 (pp20) REVERT: B 39 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8826 (tm-30) REVERT: B 104 ILE cc_start: 0.9250 (tp) cc_final: 0.9022 (tp) REVERT: B 126 PHE cc_start: 0.8866 (t80) cc_final: 0.8419 (t80) REVERT: B 185 PHE cc_start: 0.9209 (m-10) cc_final: 0.8887 (m-10) REVERT: B 203 ASP cc_start: 0.8535 (m-30) cc_final: 0.7564 (m-30) REVERT: B 220 TYR cc_start: 0.9511 (m-80) cc_final: 0.8731 (m-80) REVERT: A 17 TYR cc_start: 0.8678 (t80) cc_final: 0.8458 (t80) REVERT: A 122 PHE cc_start: 0.8894 (t80) cc_final: 0.8550 (t80) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0411 time to fit residues: 7.3215 Evaluate side-chains 118 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 22 optimal weight: 0.0070 overall best weight: 0.3254 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.108500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092206 restraints weight = 15597.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094546 restraints weight = 10059.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.096262 restraints weight = 7242.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097407 restraints weight = 5592.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.098394 restraints weight = 4589.799| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4145 Z= 0.120 Angle : 0.705 7.856 5684 Z= 0.322 Chirality : 0.038 0.125 691 Planarity : 0.004 0.041 697 Dihedral : 3.780 16.791 571 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.38), residues: 523 helix: 2.28 (0.26), residues: 403 sheet: None (None), residues: 0 loop : -1.49 (0.62), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 166 TYR 0.018 0.002 TYR B 206 PHE 0.015 0.001 PHE A 185 TRP 0.014 0.001 TRP B 199 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 4144) covalent geometry : angle 0.70497 / 0.32 ( 5682) SS BOND : bond 0.00044 / 0.03 ( 1) SS BOND : angle 0.50546 / 0.24 ( 2) hydrogen bonds : bond 0.03573 / 2.38 ( 305) hydrogen bonds : angle 3.42770 / 2.57 ( 915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 894.99 seconds wall clock time: 16 minutes 10.56 seconds (970.56 seconds total)