Starting phenix.real_space_refine on Tue Aug 4 15:00:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22of_68536/08_2026/22of_68536.cif Found real_map, /net/cci-nas-00/data/ceres_data/22of_68536/08_2026/22of_68536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22of_68536/08_2026/22of_68536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22of_68536/08_2026/22of_68536.map" model { file = "/net/cci-nas-00/data/ceres_data/22of_68536/08_2026/22of_68536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22of_68536/08_2026/22of_68536.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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 P 3 5.49 5 S 13 5.16 5 C 2719 2.51 5 N 653 2.21 5 O 705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4093 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2401 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 20, 'TRANS': 285} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1644 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 198} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.10, per 1000 atoms: 0.27 Number of scatterers: 4093 At special positions: 0 Unit cell: (92.65, 68.85, 90.95, 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) S 13 16.00 P 3 15.00 O 705 8.00 N 653 7.00 C 2719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.36 Conformation dependent library (CDL) restraints added in 157.6 milliseconds 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 2 sheets defined 67.8% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.859A pdb=" N GLY A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 Proline residue: A 104 - end of helix Processing helix chain 'A' and resid 124 through 147 Processing helix chain 'A' and resid 158 through 180 removed outlier: 3.602A pdb=" N PHE A 178 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 219 removed outlier: 3.665A pdb=" N ARG A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 4.964A pdb=" N LEU A 239 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 263 removed outlier: 3.801A pdb=" N THR A 249 " --> pdb=" O CYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 293 Processing helix chain 'B' and resid 3 through 31 removed outlier: 3.583A pdb=" N ASN B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 41 removed outlier: 3.514A pdb=" N SER B 41 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 53 Processing helix chain 'B' and resid 53 through 63 removed outlier: 4.307A pdb=" N VAL B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 84 removed outlier: 3.811A pdb=" N THR B 72 " --> pdb=" O PRO B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.865A pdb=" N ARG B 94 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 96 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 122 Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.627A pdb=" N LEU B 131 " --> pdb=" O PRO B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 164 Proline residue: B 143 - end of helix removed outlier: 4.527A pdb=" N ASN B 158 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 210 removed outlier: 3.883A pdb=" N ILE B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Proline residue: B 193 - end of helix Proline residue: B 196 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 removed outlier: 7.023A pdb=" N LEU A 16 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASP A 9 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 75 " --> pdb=" O ILE A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87 removed outlier: 3.638A pdb=" N ILE A 86 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET A 156 " --> pdb=" O ILE A 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 258 hydrogen bonds defined for protein. 756 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: 0.62 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 629 1.32 - 1.44: 1217 1.44 - 1.57: 2343 1.57 - 1.69: 4 1.69 - 1.81: 25 Bond restraints: 4218 Sorted by residual: bond pdb=" C1B NDP A 401 " pdb=" N9A NDP A 401 " ideal model delta sigma weight residual 1.470 1.590 -0.120 3.40e-02 8.65e+02 1.25e+01 bond pdb=" N PRO B 196 " pdb=" CA PRO B 196 " ideal model delta sigma weight residual 1.472 1.426 0.046 1.32e-02 5.74e+03 1.22e+01 bond pdb=" N PRO B 196 " pdb=" CD PRO B 196 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.14e+01 bond pdb=" N LYS B 207 " pdb=" CA LYS B 207 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.51e+00 bond pdb=" O1N NDP A 401 " pdb=" PN NDP A 401 " ideal model delta sigma weight residual 1.477 1.499 -0.022 1.00e-02 1.00e+04 5.04e+00 ... (remaining 4213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.63: 5760 6.63 - 13.26: 15 13.26 - 19.89: 0 19.89 - 26.52: 1 26.52 - 33.15: 1 Bond angle restraints: 5777 Sorted by residual: angle pdb=" PA NDP A 401 " pdb=" O3 NDP A 401 " pdb=" PN NDP A 401 " ideal model delta sigma weight residual 107.74 140.89 -33.15 1.95e+00 2.62e-01 2.88e+02 angle pdb=" C5B NDP A 401 " pdb=" O5B NDP A 401 " pdb=" PA NDP A 401 " ideal model delta sigma weight residual 103.84 125.54 -21.70 1.91e+00 2.73e-01 1.28e+02 angle pdb=" C5D NDP A 401 " pdb=" O5D NDP A 401 " pdb=" PN NDP A 401 " ideal model delta sigma weight residual 104.93 118.18 -13.25 2.66e+00 1.41e-01 2.48e+01 angle pdb=" O3 NDP A 401 " pdb=" PA NDP A 401 " pdb=" O5B NDP A 401 " ideal model delta sigma weight residual 108.94 96.95 11.99 2.49e+00 1.62e-01 2.33e+01 angle pdb=" N PRO A 157 " pdb=" CA PRO A 157 " pdb=" C PRO A 157 " ideal model delta sigma weight residual 110.40 117.83 -7.43 1.61e+00 3.86e-01 2.13e+01 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 2351 35.65 - 71.30: 67 71.30 - 106.94: 5 106.94 - 142.59: 0 142.59 - 178.24: 1 Dihedral angle restraints: 2424 sinusoidal: 910 harmonic: 1514 Sorted by residual: dihedral pdb=" CA LEU B 174 " pdb=" C LEU B 174 " pdb=" N ASN B 175 " pdb=" CA ASN B 175 " ideal model delta harmonic sigma weight residual -180.00 -151.51 -28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" C5B NDP A 401 " pdb=" O5B NDP A 401 " pdb=" PA NDP A 401 " pdb=" O3 NDP A 401 " ideal model delta sinusoidal sigma weight residual 175.04 -6.72 -178.24 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C LYS B 207 " pdb=" N LYS B 207 " pdb=" CA LYS B 207 " pdb=" CB LYS B 207 " ideal model delta harmonic sigma weight residual -122.60 -113.89 -8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 2421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 550 0.054 - 0.109: 95 0.109 - 0.163: 12 0.163 - 0.218: 1 0.218 - 0.272: 4 Chirality restraints: 662 Sorted by residual: chirality pdb=" C1D NDP A 401 " pdb=" C2D NDP A 401 " pdb=" N1N NDP A 401 " pdb=" O4D NDP A 401 " both_signs ideal model delta sigma weight residual False 2.60 2.33 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C2D NDP A 401 " pdb=" C1D NDP A 401 " pdb=" C3D NDP A 401 " pdb=" O2D NDP A 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.96 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU A 214 " pdb=" CB LEU A 214 " pdb=" CD1 LEU A 214 " pdb=" CD2 LEU A 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 659 not shown) Planarity restraints: 710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 401 " -0.335 2.00e-02 2.50e+03 2.31e-01 6.69e+02 pdb=" C3N NDP A 401 " -0.172 2.00e-02 2.50e+03 pdb=" C4N NDP A 401 " 0.008 2.00e-02 2.50e+03 pdb=" C7N NDP A 401 " 0.215 2.00e-02 2.50e+03 pdb=" N1N NDP A 401 " 0.283 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 401 " 0.049 2.00e-02 2.50e+03 8.46e-02 7.16e+01 pdb=" C5N NDP A 401 " -0.108 2.00e-02 2.50e+03 pdb=" C6N NDP A 401 " 0.109 2.00e-02 2.50e+03 pdb=" N1N NDP A 401 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 157 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C PRO A 157 " 0.043 2.00e-02 2.50e+03 pdb=" O PRO A 157 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 158 " -0.015 2.00e-02 2.50e+03 ... (remaining 707 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 536 2.75 - 3.29: 4189 3.29 - 3.82: 6989 3.82 - 4.36: 7320 4.36 - 4.90: 12630 Nonbonded interactions: 31664 Sorted by model distance: nonbonded pdb=" OE1 GLU B 149 " pdb=" OH TYR B 191 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR A 44 " pdb=" OE1 GLU A 45 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLU A 144 " pdb=" ND1 HIS A 212 " model vdw 2.275 3.120 nonbonded pdb=" ND1 HIS A 137 " pdb=" OE2 GLU A 205 " model vdw 2.295 3.120 nonbonded pdb=" O ALA A 49 " pdb=" NH2 ARG A 51 " model vdw 2.306 3.120 ... (remaining 31659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.660 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.005 0.120 4218 Z= 0.218 Angle : 1.006 33.148 5777 Z= 0.513 Chirality : 0.046 0.272 662 Planarity : 0.011 0.231 710 Dihedral : 16.888 178.237 1452 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.72 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 20.33 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.67 (0.38), residues: 511 helix: 1.91 (0.29), residues: 317 sheet: 1.27 (1.21), residues: 23 loop : -0.41 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 113 TYR 0.014 0.001 TYR B 39 PHE 0.022 0.001 PHE A 143 TRP 0.017 0.002 TRP B 182 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 ( 4218) covalent geometry : angle 1.00581 / 0.51 ( 5777) hydrogen bonds : bond 0.10467 / 7.22 ( 258) hydrogen bonds : angle 4.42062 / 3.08 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7812 (mttm) REVERT: A 227 ARG cc_start: 0.6849 (mtm180) cc_final: 0.6588 (mtt90) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0987 time to fit residues: 9.5843 Evaluate side-chains 78 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.0370 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.199582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.148289 restraints weight = 6018.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152403 restraints weight = 3339.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.155003 restraints weight = 2374.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.156094 restraints weight = 1955.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157188 restraints weight = 1776.615| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4218 Z= 0.135 Angle : 0.587 5.339 5777 Z= 0.297 Chirality : 0.040 0.124 662 Planarity : 0.005 0.033 710 Dihedral : 9.127 174.959 570 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.91 % Favored : 95.89 % Rotamer: Outliers : 3.83 % Allowed : 19.38 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.76 (0.38), residues: 511 helix: 2.05 (0.29), residues: 319 sheet: 0.71 (1.13), residues: 23 loop : -0.48 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 113 TYR 0.015 0.001 TYR A 114 PHE 0.008 0.001 PHE A 143 TRP 0.010 0.001 TRP B 182 HIS 0.004 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4218) covalent geometry : angle 0.58727 / 0.30 ( 5777) hydrogen bonds : bond 0.04551 / 3.04 ( 258) hydrogen bonds : angle 3.98304 / 2.85 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8292 (mp) cc_final: 0.8078 (mp) REVERT: A 230 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8302 (ttmm) REVERT: A 239 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8049 (tt) REVERT: B 114 TYR cc_start: 0.7969 (m-80) cc_final: 0.7728 (m-80) outliers start: 16 outliers final: 11 residues processed: 100 average time/residue: 0.0740 time to fit residues: 8.9216 Evaluate side-chains 96 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 208 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 0.0000 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 2 optimal weight: 20.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.192472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.141928 restraints weight = 5627.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.145904 restraints weight = 3169.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148457 restraints weight = 2279.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149971 restraints weight = 1882.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150610 restraints weight = 1685.331| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4218 Z= 0.122 Angle : 0.555 5.964 5777 Z= 0.283 Chirality : 0.040 0.120 662 Planarity : 0.005 0.033 710 Dihedral : 8.984 174.157 570 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.52 % Favored : 96.28 % Rotamer: Outliers : 4.55 % Allowed : 18.42 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.89 (0.38), residues: 511 helix: 2.15 (0.29), residues: 318 sheet: 0.61 (1.11), residues: 23 loop : -0.36 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 300 TYR 0.011 0.001 TYR A 114 PHE 0.008 0.001 PHE B 116 TRP 0.010 0.001 TRP A 134 HIS 0.003 0.000 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 4218) covalent geometry : angle 0.55463 / 0.28 ( 5777) hydrogen bonds : bond 0.04177 / 2.81 ( 258) hydrogen bonds : angle 3.83597 / 2.74 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.7975 (mttm) cc_final: 0.7716 (mmtt) REVERT: A 85 GLN cc_start: 0.6095 (mm-40) cc_final: 0.5781 (mm-40) REVERT: A 239 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8211 (tt) REVERT: A 243 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8834 (t) REVERT: B 114 TYR cc_start: 0.8036 (m-80) cc_final: 0.7828 (m-80) outliers start: 19 outliers final: 13 residues processed: 101 average time/residue: 0.0541 time to fit residues: 6.6065 Evaluate side-chains 100 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 165 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 30.0000 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.188373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137809 restraints weight = 5635.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.141459 restraints weight = 3303.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.143825 restraints weight = 2429.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.145130 restraints weight = 2032.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145614 restraints weight = 1836.253| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4218 Z= 0.148 Angle : 0.591 6.455 5777 Z= 0.302 Chirality : 0.041 0.126 662 Planarity : 0.005 0.034 710 Dihedral : 8.642 165.265 570 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.33 % Favored : 96.48 % Rotamer: Outliers : 5.26 % Allowed : 19.38 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.90 (0.38), residues: 511 helix: 2.06 (0.29), residues: 319 sheet: 0.80 (1.14), residues: 23 loop : -0.19 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 35 TYR 0.015 0.001 TYR B 117 PHE 0.016 0.001 PHE B 195 TRP 0.012 0.001 TRP B 182 HIS 0.004 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 4218) covalent geometry : angle 0.59145 / 0.30 ( 5777) hydrogen bonds : bond 0.04553 / 3.05 ( 258) hydrogen bonds : angle 3.88781 / 2.77 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.4145 (mmmm) cc_final: 0.3817 (mtpt) REVERT: A 206 PHE cc_start: 0.7931 (m-80) cc_final: 0.7685 (m-10) REVERT: A 214 LEU cc_start: 0.8241 (mp) cc_final: 0.7928 (mp) REVERT: A 227 ARG cc_start: 0.6943 (mtt90) cc_final: 0.6724 (mtt90) REVERT: A 230 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8527 (mttm) REVERT: A 239 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8357 (tt) outliers start: 22 outliers final: 15 residues processed: 97 average time/residue: 0.0597 time to fit residues: 6.9698 Evaluate side-chains 97 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 192 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.0770 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.0010 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 146 GLN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.191960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.141737 restraints weight = 5527.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.145563 restraints weight = 3218.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148105 restraints weight = 2349.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149411 restraints weight = 1944.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.150359 restraints weight = 1752.090| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4218 Z= 0.111 Angle : 0.552 6.078 5777 Z= 0.280 Chirality : 0.039 0.127 662 Planarity : 0.004 0.033 710 Dihedral : 8.552 164.327 570 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.13 % Favored : 96.67 % Rotamer: Outliers : 4.31 % Allowed : 22.73 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.03 (0.38), residues: 511 helix: 2.19 (0.29), residues: 319 sheet: 0.84 (1.14), residues: 23 loop : -0.19 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 300 TYR 0.008 0.001 TYR A 114 PHE 0.012 0.001 PHE B 195 TRP 0.008 0.001 TRP A 134 HIS 0.002 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 4218) covalent geometry : angle 0.55161 / 0.28 ( 5777) hydrogen bonds : bond 0.03862 / 2.59 ( 258) hydrogen bonds : angle 3.73702 / 2.67 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.4007 (mmmm) cc_final: 0.3708 (mtpt) REVERT: A 214 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8071 (mp) REVERT: B 206 ARG cc_start: 0.7989 (tmm-80) cc_final: 0.7687 (tmm-80) outliers start: 18 outliers final: 13 residues processed: 98 average time/residue: 0.0668 time to fit residues: 7.9385 Evaluate side-chains 96 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 208 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.0770 chunk 4 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.188927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.138824 restraints weight = 5663.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142385 restraints weight = 3388.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144650 restraints weight = 2523.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.145888 restraints weight = 2123.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146688 restraints weight = 1929.809| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4218 Z= 0.131 Angle : 0.572 7.551 5777 Z= 0.291 Chirality : 0.040 0.138 662 Planarity : 0.005 0.076 710 Dihedral : 8.491 163.427 570 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.94 % Favored : 96.87 % Rotamer: Outliers : 4.07 % Allowed : 24.16 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.09 (0.38), residues: 511 helix: 2.15 (0.29), residues: 320 sheet: 0.92 (1.14), residues: 23 loop : -0.01 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 35 TYR 0.012 0.001 TYR A 242 PHE 0.018 0.001 PHE B 116 TRP 0.012 0.001 TRP A 134 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 4218) covalent geometry : angle 0.57191 / 0.29 ( 5777) hydrogen bonds : bond 0.04153 / 2.77 ( 258) hydrogen bonds : angle 3.77914 / 2.71 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7590 (tp) cc_final: 0.7020 (mp) REVERT: A 214 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7935 (mp) outliers start: 17 outliers final: 12 residues processed: 100 average time/residue: 0.0588 time to fit residues: 7.2670 Evaluate side-chains 97 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 191 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.192956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.142283 restraints weight = 5746.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146314 restraints weight = 3127.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.148808 restraints weight = 2213.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.150107 restraints weight = 1817.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.150887 restraints weight = 1638.053| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4218 Z= 0.146 Angle : 0.606 7.011 5777 Z= 0.312 Chirality : 0.040 0.125 662 Planarity : 0.005 0.061 710 Dihedral : 8.521 163.882 570 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.13 % Favored : 96.67 % Rotamer: Outliers : 4.07 % Allowed : 25.12 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.02 (0.38), residues: 511 helix: 2.03 (0.29), residues: 321 sheet: 0.93 (1.13), residues: 23 loop : 0.10 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 35 TYR 0.013 0.001 TYR A 296 PHE 0.012 0.001 PHE A 293 TRP 0.012 0.001 TRP A 134 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 4218) covalent geometry : angle 0.60557 / 0.31 ( 5777) hydrogen bonds : bond 0.04438 / 2.97 ( 258) hydrogen bonds : angle 3.81956 / 2.74 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7703 (tp) cc_final: 0.7208 (mp) REVERT: A 214 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7914 (mp) outliers start: 17 outliers final: 15 residues processed: 91 average time/residue: 0.0689 time to fit residues: 7.7115 Evaluate side-chains 97 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 191 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 0.0470 chunk 42 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.194343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.144022 restraints weight = 5617.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.148044 restraints weight = 3045.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.150495 restraints weight = 2148.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.151948 restraints weight = 1766.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.152415 restraints weight = 1582.569| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4218 Z= 0.129 Angle : 0.584 6.413 5777 Z= 0.296 Chirality : 0.040 0.123 662 Planarity : 0.005 0.052 710 Dihedral : 8.481 163.656 570 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.74 % Favored : 97.06 % Rotamer: Outliers : 4.55 % Allowed : 24.64 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.05 (0.38), residues: 511 helix: 2.07 (0.29), residues: 321 sheet: 1.03 (1.17), residues: 23 loop : 0.07 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 35 TYR 0.011 0.001 TYR A 114 PHE 0.010 0.001 PHE A 240 TRP 0.010 0.001 TRP A 134 HIS 0.002 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 4218) covalent geometry : angle 0.58420 / 0.30 ( 5777) hydrogen bonds : bond 0.04176 / 2.79 ( 258) hydrogen bonds : angle 3.77174 / 2.70 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7714 (tp) cc_final: 0.7198 (mp) REVERT: A 34 LYS cc_start: 0.8320 (ptpt) cc_final: 0.7751 (ptmt) REVERT: A 214 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7943 (mp) REVERT: B 206 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7955 (tmm-80) outliers start: 19 outliers final: 16 residues processed: 96 average time/residue: 0.0715 time to fit residues: 8.4953 Evaluate side-chains 100 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 192 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.191468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.140955 restraints weight = 5699.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.144903 restraints weight = 3119.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.147296 restraints weight = 2217.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.148550 restraints weight = 1832.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.149510 restraints weight = 1655.659| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4218 Z= 0.153 Angle : 0.627 7.149 5777 Z= 0.316 Chirality : 0.041 0.213 662 Planarity : 0.005 0.048 710 Dihedral : 8.477 163.638 570 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.13 % Favored : 96.67 % Rotamer: Outliers : 4.07 % Allowed : 24.88 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.89 (0.38), residues: 511 helix: 1.99 (0.29), residues: 320 sheet: 1.04 (1.17), residues: 23 loop : -0.10 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 35 TYR 0.012 0.001 TYR A 114 PHE 0.013 0.001 PHE A 270 TRP 0.013 0.002 TRP A 134 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 4218) covalent geometry : angle 0.62697 / 0.32 ( 5777) hydrogen bonds : bond 0.04589 / 3.07 ( 258) hydrogen bonds : angle 3.88505 / 2.78 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7698 (tp) cc_final: 0.7200 (mp) REVERT: A 214 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7975 (mp) REVERT: B 162 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 206 ARG cc_start: 0.8180 (tmm-80) cc_final: 0.7975 (tmm-80) outliers start: 17 outliers final: 14 residues processed: 94 average time/residue: 0.0705 time to fit residues: 8.1898 Evaluate side-chains 98 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 192 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 40.0000 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.192547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.142397 restraints weight = 5571.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.146265 restraints weight = 3081.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.148667 restraints weight = 2202.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.149688 restraints weight = 1823.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.150837 restraints weight = 1664.095| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4218 Z= 0.138 Angle : 0.617 8.310 5777 Z= 0.310 Chirality : 0.041 0.179 662 Planarity : 0.005 0.045 710 Dihedral : 8.448 163.644 570 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.13 % Favored : 96.67 % Rotamer: Outliers : 3.59 % Allowed : 26.79 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.91 (0.38), residues: 511 helix: 2.01 (0.29), residues: 320 sheet: 1.15 (1.18), residues: 23 loop : -0.13 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.012 0.001 TYR A 114 PHE 0.012 0.001 PHE A 240 TRP 0.010 0.001 TRP A 134 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 4218) covalent geometry : angle 0.61682 / 0.31 ( 5777) hydrogen bonds : bond 0.04409 / 2.94 ( 258) hydrogen bonds : angle 3.85557 / 2.75 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7719 (tp) cc_final: 0.7222 (mp) REVERT: A 214 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7972 (mp) REVERT: B 162 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7800 (tm-30) outliers start: 15 outliers final: 14 residues processed: 93 average time/residue: 0.0661 time to fit residues: 7.6028 Evaluate side-chains 99 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 192 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.191333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.141143 restraints weight = 5673.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.144989 restraints weight = 3120.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.147403 restraints weight = 2231.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.148628 restraints weight = 1846.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.149589 restraints weight = 1668.058| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4218 Z= 0.148 Angle : 0.613 6.861 5777 Z= 0.312 Chirality : 0.041 0.166 662 Planarity : 0.005 0.044 710 Dihedral : 8.437 163.461 570 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.52 % Favored : 96.28 % Rotamer: Outliers : 3.83 % Allowed : 25.84 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.84 (0.38), residues: 511 helix: 1.95 (0.29), residues: 320 sheet: 1.20 (1.20), residues: 23 loop : -0.15 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 35 TYR 0.013 0.001 TYR A 114 PHE 0.011 0.001 PHE A 270 TRP 0.012 0.001 TRP A 134 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 4218) covalent geometry : angle 0.61343 / 0.31 ( 5777) hydrogen bonds : bond 0.04472 / 2.98 ( 258) hydrogen bonds : angle 3.87505 / 2.76 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 799.02 seconds wall clock time: 14 minutes 24.54 seconds (864.54 seconds total)