Starting phenix.real_space_refine on Tue Aug 4 14:57:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ovd_70898/08_2026/9ovd_70898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ovd_70898/08_2026/9ovd_70898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ovd_70898/08_2026/9ovd_70898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ovd_70898/08_2026/9ovd_70898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ovd_70898/08_2026/9ovd_70898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ovd_70898/08_2026/9ovd_70898.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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 4 8.98 5 S 16 5.16 5 C 2750 2.51 5 N 662 2.21 5 O 696 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: 4128 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" 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: "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: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {' K': 1, 'LBN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.32, per 1000 atoms: 0.32 Number of scatterers: 4128 At special positions: 0 Unit cell: (67.08, 79.12, 98.9, 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 4 19.00 S 16 16.00 O 696 8.00 N 662 7.00 C 2750 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: 0.32 Conformation dependent library (CDL) restraints added in 156.5 milliseconds 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 75.9% 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: 4.067A pdb=" N ALA B 8 " --> pdb=" O GLY B 4 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 4.042A 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 Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 116 through 152 Proline residue: B 132 - end of helix removed outlier: 4.066A pdb=" N VAL B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 185 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 201 through 211 removed outlier: 3.519A pdb=" N PHE B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 264 removed outlier: 3.538A pdb=" N PHE B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.740A 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 removed outlier: 3.585A pdb=" N ALA A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 51 removed outlier: 4.255A pdb=" N ALA A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.786A pdb=" N LEU A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 116 through 150 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 167 through 194 Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 230 through 263 removed outlier: 3.934A pdb=" N HIS A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 270 removed outlier: 4.242A pdb=" N LEU A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 897 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: 0.70 Time building geometry restraints manager: 0.43 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: 666 1.32 - 1.45: 1111 1.45 - 1.57: 2431 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4230 Sorted by residual: bond pdb=" C ALA A 56 " pdb=" N PRO A 57 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.18e-01 bond pdb=" CB GLN B 46 " pdb=" CG GLN B 46 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.60e-01 bond pdb=" C VAL B 131 " pdb=" N PRO B 132 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.23e-01 bond pdb=" CB ARG B 35 " pdb=" CG ARG B 35 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.38e-01 bond pdb=" CG PRO B 272 " pdb=" CD PRO B 272 " ideal model delta sigma weight residual 1.503 1.527 -0.024 3.40e-02 8.65e+02 4.88e-01 ... (remaining 4225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 5560 1.24 - 2.47: 158 2.47 - 3.71: 36 3.71 - 4.94: 12 4.94 - 6.18: 8 Bond angle restraints: 5774 Sorted by residual: angle pdb=" C SER B 200 " pdb=" N PHE B 201 " pdb=" CA PHE B 201 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.42e+00 angle pdb=" C LEU A 186 " pdb=" N VAL A 187 " pdb=" CA VAL A 187 " ideal model delta sigma weight residual 122.13 118.10 4.03 1.85e+00 2.92e-01 4.75e+00 angle pdb=" CA GLN B 46 " pdb=" CB GLN B 46 " pdb=" CG GLN B 46 " ideal model delta sigma weight residual 114.10 118.41 -4.31 2.00e+00 2.50e-01 4.64e+00 angle pdb=" N GLY B 30 " pdb=" CA GLY B 30 " pdb=" C GLY B 30 " ideal model delta sigma weight residual 112.34 116.67 -4.33 2.04e+00 2.40e-01 4.51e+00 angle pdb=" C THR B 105 " pdb=" N THR B 106 " pdb=" CA THR B 106 " ideal model delta sigma weight residual 122.36 125.45 -3.09 1.47e+00 4.63e-01 4.42e+00 ... (remaining 5769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.80: 2280 26.80 - 53.60: 166 53.60 - 80.40: 19 80.40 - 107.20: 1 107.20 - 134.01: 1 Dihedral angle restraints: 2467 sinusoidal: 929 harmonic: 1538 Sorted by residual: dihedral pdb=" CB CYS B 53 " pdb=" SG CYS B 53 " pdb=" SG CYS A 53 " pdb=" CB CYS A 53 " ideal model delta sinusoidal sigma weight residual 93.00 162.19 -69.19 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" O5 LBN B 301 " pdb=" C2 LBN B 301 " pdb=" C3 LBN B 301 " pdb=" O7 LBN B 301 " ideal model delta sinusoidal sigma weight residual 62.67 -71.34 134.01 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" CA TRP A 156 " pdb=" C TRP A 156 " pdb=" N LEU A 157 " pdb=" CA LEU A 157 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 2464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 496 0.033 - 0.065: 147 0.065 - 0.098: 29 0.098 - 0.130: 17 0.130 - 0.163: 3 Chirality restraints: 692 Sorted by residual: chirality pdb=" CB VAL A 54 " pdb=" CA VAL A 54 " pdb=" CG1 VAL A 54 " pdb=" CG2 VAL A 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CB VAL B 66 " pdb=" CA VAL B 66 " pdb=" CG1 VAL B 66 " pdb=" CG2 VAL B 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA VAL A 54 " pdb=" N VAL A 54 " pdb=" C VAL A 54 " pdb=" CB VAL A 54 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 689 not shown) Planarity restraints: 706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 156 " 0.019 2.00e-02 2.50e+03 1.25e-02 3.90e+00 pdb=" CG TRP A 156 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 156 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 156 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 156 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 156 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 156 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 156 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 156 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 156 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 201 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C PHE B 201 " -0.027 2.00e-02 2.50e+03 pdb=" O PHE B 201 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU B 202 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 105 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.43e+00 pdb=" C THR B 105 " 0.027 2.00e-02 2.50e+03 pdb=" O THR B 105 " -0.010 2.00e-02 2.50e+03 pdb=" N THR B 106 " -0.009 2.00e-02 2.50e+03 ... (remaining 703 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.07: 2797 3.07 - 3.59: 5134 3.59 - 4.11: 6037 4.11 - 4.62: 9698 4.62 - 5.14: 12058 Nonbonded interactions: 35724 Sorted by model distance: nonbonded pdb=" O THR B 105 " pdb=" OG1 THR B 106 " model vdw 2.553 3.040 nonbonded pdb=" K K A 302 " pdb=" K K A 303 " model vdw 2.587 2.660 nonbonded pdb=" O THR A 105 " pdb=" OG1 THR A 106 " model vdw 2.592 3.040 nonbonded pdb=" O THR B 106 " pdb=" OG1 THR B 106 " model vdw 2.593 3.040 nonbonded pdb=" N VAL A 54 " pdb=" O VAL A 54 " model vdw 2.602 2.496 ... (remaining 35719 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 275 or resid 303)) selection = (chain 'B' and (resid 4 through 275 or resid 303)) } 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.460 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4231 Z= 0.124 Angle : 0.571 6.176 5776 Z= 0.283 Chirality : 0.036 0.163 692 Planarity : 0.004 0.030 706 Dihedral : 17.608 134.005 1472 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.11 % Favored : 93.70 % Rotamer: Outliers : 3.14 % Allowed : 30.19 % Favored : 66.67 % 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: 2.47 (0.39), residues: 524 helix: 2.74 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -2.30 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 35 TYR 0.010 0.001 TYR A 230 PHE 0.009 0.001 PHE B 126 TRP 0.033 0.001 TRP A 156 HIS 0.002 0.000 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 4230) covalent geometry : angle 0.57012 / 0.28 ( 5774) SS BOND : bond 0.00151 / 0.09 ( 1) SS BOND : angle 1.41155 / 0.63 ( 2) hydrogen bonds : bond 0.09798 / 6.81 ( 299) hydrogen bonds : angle 4.13440 / 3.06 ( 897) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.148 Fit side-chains REVERT: A 20 LEU cc_start: 0.8147 (mm) cc_final: 0.6959 (tp) REVERT: A 64 GLU cc_start: 0.8716 (tt0) cc_final: 0.8076 (tp30) REVERT: A 133 THR cc_start: 0.7437 (OUTLIER) cc_final: 0.6803 (t) REVERT: A 134 THR cc_start: 0.8380 (p) cc_final: 0.8092 (m) REVERT: A 249 MET cc_start: 0.7387 (tpt) cc_final: 0.7098 (tpt) outliers start: 13 outliers final: 10 residues processed: 75 average time/residue: 0.0469 time to fit residues: 4.9774 Evaluate side-chains 73 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 268 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** 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 = 0.4601 r_free = 0.4601 target = 0.233514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.189175 restraints weight = 5651.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.192127 restraints weight = 5683.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.193681 restraints weight = 4631.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.193661 restraints weight = 3312.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.194056 restraints weight = 3667.856| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4231 Z= 0.123 Angle : 0.535 5.399 5776 Z= 0.268 Chirality : 0.035 0.128 692 Planarity : 0.004 0.027 706 Dihedral : 12.001 112.240 656 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.73 % Favored : 94.08 % Rotamer: Outliers : 6.04 % Allowed : 28.02 % Favored : 65.94 % 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: 2.68 (0.39), residues: 524 helix: 2.78 (0.26), residues: 402 sheet: None (None), residues: 0 loop : -1.92 (0.61), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 35 TYR 0.010 0.001 TYR B 17 PHE 0.016 0.001 PHE B 126 TRP 0.024 0.001 TRP A 156 HIS 0.005 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 4230) covalent geometry : angle 0.53413 / 0.27 ( 5774) SS BOND : bond 0.00062 / 0.04 ( 1) SS BOND : angle 1.26598 / 0.58 ( 2) hydrogen bonds : bond 0.04427 / 3.02 ( 299) hydrogen bonds : angle 3.63507 / 2.69 ( 897) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.193 Fit side-chains REVERT: A 7 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8176 (mp) REVERT: A 20 LEU cc_start: 0.8015 (mm) cc_final: 0.6935 (tp) REVERT: A 35 ARG cc_start: 0.7558 (mpt180) cc_final: 0.7178 (mmt-90) REVERT: A 64 GLU cc_start: 0.8824 (tt0) cc_final: 0.8117 (tp30) REVERT: A 133 THR cc_start: 0.7355 (OUTLIER) cc_final: 0.6738 (t) REVERT: A 134 THR cc_start: 0.8418 (p) cc_final: 0.8193 (m) REVERT: A 249 MET cc_start: 0.7333 (tpt) cc_final: 0.7028 (tpt) outliers start: 25 outliers final: 18 residues processed: 85 average time/residue: 0.0510 time to fit residues: 5.9802 Evaluate side-chains 85 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 267 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.0060 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 = 0.4613 r_free = 0.4613 target = 0.234842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.189774 restraints weight = 5652.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.190872 restraints weight = 5993.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.192030 restraints weight = 5458.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.192314 restraints weight = 3829.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.193209 restraints weight = 3314.233| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4231 Z= 0.131 Angle : 0.562 7.168 5776 Z= 0.277 Chirality : 0.036 0.131 692 Planarity : 0.004 0.029 706 Dihedral : 11.543 94.278 649 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.15 % Favored : 94.66 % Rotamer: Outliers : 6.76 % Allowed : 28.50 % Favored : 64.73 % 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: 2.72 (0.39), residues: 524 helix: 2.77 (0.26), residues: 402 sheet: None (None), residues: 0 loop : -1.76 (0.62), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.010 0.001 TYR B 17 PHE 0.009 0.001 PHE A 207 TRP 0.018 0.001 TRP A 156 HIS 0.005 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 4230) covalent geometry : angle 0.56223 / 0.28 ( 5774) SS BOND : bond 0.00039 / 0.02 ( 1) SS BOND : angle 1.02676 / 0.47 ( 2) hydrogen bonds : bond 0.04431 / 3.03 ( 299) hydrogen bonds : angle 3.58169 / 2.66 ( 897) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 20 LEU cc_start: 0.7992 (mm) cc_final: 0.6917 (tp) REVERT: A 35 ARG cc_start: 0.7579 (mpt180) cc_final: 0.7159 (mmt-90) REVERT: A 64 GLU cc_start: 0.8881 (tt0) cc_final: 0.8136 (tp30) REVERT: A 133 THR cc_start: 0.7365 (OUTLIER) cc_final: 0.6772 (t) REVERT: A 134 THR cc_start: 0.8467 (p) cc_final: 0.8210 (m) REVERT: A 249 MET cc_start: 0.7330 (tpt) cc_final: 0.7046 (tpt) outliers start: 28 outliers final: 18 residues processed: 90 average time/residue: 0.0476 time to fit residues: 5.9415 Evaluate side-chains 88 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4623 r_free = 0.4623 target = 0.235377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.196093 restraints weight = 5621.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.200743 restraints weight = 5702.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.198457 restraints weight = 3334.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.199111 restraints weight = 3364.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.199064 restraints weight = 2803.552| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4231 Z= 0.129 Angle : 0.565 7.629 5776 Z= 0.279 Chirality : 0.036 0.122 692 Planarity : 0.004 0.029 706 Dihedral : 11.117 76.904 647 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.92 % Favored : 93.89 % Rotamer: Outliers : 7.49 % Allowed : 27.54 % Favored : 64.98 % 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: 2.78 (0.39), residues: 524 helix: 2.79 (0.26), residues: 402 sheet: None (None), residues: 0 loop : -1.64 (0.64), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 35 TYR 0.010 0.001 TYR B 17 PHE 0.009 0.001 PHE A 207 TRP 0.020 0.001 TRP A 156 HIS 0.005 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 4230) covalent geometry : angle 0.56460 / 0.28 ( 5774) SS BOND : bond 0.00022 / 0.01 ( 1) SS BOND : angle 0.94011 / 0.43 ( 2) hydrogen bonds : bond 0.04303 / 2.94 ( 299) hydrogen bonds : angle 3.55508 / 2.64 ( 897) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8197 (mp) REVERT: A 20 LEU cc_start: 0.7973 (mm) cc_final: 0.6917 (tp) REVERT: A 35 ARG cc_start: 0.7518 (mpt180) cc_final: 0.7133 (mmt-90) REVERT: A 64 GLU cc_start: 0.8775 (tt0) cc_final: 0.8117 (tp30) outliers start: 31 outliers final: 26 residues processed: 92 average time/residue: 0.0410 time to fit residues: 5.2281 Evaluate side-chains 94 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 163 TRP Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 268 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** 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 = 0.4605 r_free = 0.4605 target = 0.233901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.189137 restraints weight = 5654.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.191407 restraints weight = 5945.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.191929 restraints weight = 4912.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.192463 restraints weight = 3624.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.192760 restraints weight = 3153.459| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4231 Z= 0.127 Angle : 0.563 6.440 5776 Z= 0.277 Chirality : 0.035 0.129 692 Planarity : 0.004 0.029 706 Dihedral : 10.588 76.225 646 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.34 % Favored : 94.47 % Rotamer: Outliers : 7.25 % Allowed : 27.29 % Favored : 65.46 % 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: 2.88 (0.40), residues: 524 helix: 2.85 (0.26), residues: 402 sheet: None (None), residues: 0 loop : -1.55 (0.65), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.011 0.001 TYR B 17 PHE 0.010 0.001 PHE B 201 TRP 0.033 0.001 TRP A 156 HIS 0.006 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 4230) covalent geometry : angle 0.56297 / 0.28 ( 5774) SS BOND : bond 0.00036 / 0.02 ( 1) SS BOND : angle 0.66461 / 0.31 ( 2) hydrogen bonds : bond 0.04281 / 2.93 ( 299) hydrogen bonds : angle 3.54054 / 2.63 ( 897) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8170 (mp) REVERT: A 20 LEU cc_start: 0.8009 (mm) cc_final: 0.6975 (tp) REVERT: A 35 ARG cc_start: 0.7604 (mpt180) cc_final: 0.7202 (mmt-90) REVERT: A 64 GLU cc_start: 0.8882 (tt0) cc_final: 0.8146 (tp30) outliers start: 30 outliers final: 25 residues processed: 91 average time/residue: 0.0462 time to fit residues: 5.8352 Evaluate side-chains 89 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 268 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 15 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4616 r_free = 0.4616 target = 0.235019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.190487 restraints weight = 5809.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.192460 restraints weight = 6312.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.193403 restraints weight = 5121.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.193347 restraints weight = 3912.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.194033 restraints weight = 3498.407| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4231 Z= 0.124 Angle : 0.560 6.304 5776 Z= 0.275 Chirality : 0.035 0.130 692 Planarity : 0.004 0.027 706 Dihedral : 10.556 75.398 646 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.53 % Favored : 94.27 % Rotamer: Outliers : 7.00 % Allowed : 26.81 % Favored : 66.18 % 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: 2.94 (0.40), residues: 524 helix: 2.84 (0.26), residues: 404 sheet: None (None), residues: 0 loop : -1.39 (0.66), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.009 0.001 TYR A 230 PHE 0.011 0.001 PHE B 126 TRP 0.030 0.001 TRP A 156 HIS 0.004 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 4230) covalent geometry : angle 0.55972 / 0.28 ( 5774) SS BOND : bond 0.00056 / 0.04 ( 1) SS BOND : angle 0.55744 / 0.26 ( 2) hydrogen bonds : bond 0.04146 / 2.85 ( 299) hydrogen bonds : angle 3.49968 / 2.60 ( 897) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8147 (mp) REVERT: A 20 LEU cc_start: 0.8003 (mm) cc_final: 0.7021 (tp) REVERT: A 35 ARG cc_start: 0.7591 (mpt180) cc_final: 0.7213 (mmt-90) REVERT: A 64 GLU cc_start: 0.8848 (tt0) cc_final: 0.8109 (tp30) REVERT: A 133 THR cc_start: 0.7416 (OUTLIER) cc_final: 0.6972 (t) REVERT: A 249 MET cc_start: 0.7263 (tpt) cc_final: 0.7028 (tpt) outliers start: 29 outliers final: 23 residues processed: 91 average time/residue: 0.0560 time to fit residues: 6.8964 Evaluate side-chains 90 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 268 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.0470 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.0270 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.4642 r_free = 0.4642 target = 0.237983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.194661 restraints weight = 5780.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.197122 restraints weight = 6199.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.197815 restraints weight = 4904.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.198333 restraints weight = 3623.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.198730 restraints weight = 3178.841| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4231 Z= 0.110 Angle : 0.537 6.300 5776 Z= 0.265 Chirality : 0.035 0.136 692 Planarity : 0.004 0.029 706 Dihedral : 10.192 73.381 646 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.73 % Favored : 94.08 % Rotamer: Outliers : 5.80 % Allowed : 29.23 % Favored : 64.98 % 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: 3.11 (0.39), residues: 524 helix: 2.92 (0.26), residues: 406 sheet: None (None), residues: 0 loop : -1.24 (0.67), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.009 0.001 TYR A 230 PHE 0.012 0.001 PHE B 126 TRP 0.027 0.001 TRP A 156 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 4230) covalent geometry : angle 0.53666 / 0.26 ( 5774) SS BOND : bond 0.00057 / 0.04 ( 1) SS BOND : angle 0.60539 / 0.29 ( 2) hydrogen bonds : bond 0.03694 / 2.52 ( 299) hydrogen bonds : angle 3.40580 / 2.52 ( 897) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.5862 (tpt-90) REVERT: A 7 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8066 (mp) REVERT: A 20 LEU cc_start: 0.7967 (mm) cc_final: 0.7058 (tp) REVERT: A 35 ARG cc_start: 0.7572 (mpt180) cc_final: 0.7199 (mmt-90) REVERT: A 64 GLU cc_start: 0.8838 (tt0) cc_final: 0.8099 (tp30) REVERT: A 133 THR cc_start: 0.7374 (OUTLIER) cc_final: 0.6918 (t) REVERT: A 249 MET cc_start: 0.7238 (tpt) cc_final: 0.7008 (tpt) outliers start: 24 outliers final: 19 residues processed: 87 average time/residue: 0.0532 time to fit residues: 6.2321 Evaluate side-chains 89 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 268 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 21 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.239312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.195893 restraints weight = 5719.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.200181 restraints weight = 5605.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.201402 restraints weight = 4524.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.201490 restraints weight = 3357.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.202550 restraints weight = 3315.295| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4231 Z= 0.107 Angle : 0.536 6.374 5776 Z= 0.262 Chirality : 0.034 0.140 692 Planarity : 0.004 0.030 706 Dihedral : 10.015 71.520 646 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.96 % Favored : 94.85 % Rotamer: Outliers : 5.31 % Allowed : 29.47 % Favored : 65.22 % 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: 3.19 (0.39), residues: 524 helix: 2.97 (0.26), residues: 406 sheet: None (None), residues: 0 loop : -1.19 (0.67), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.010 0.001 TYR A 230 PHE 0.019 0.001 PHE B 126 TRP 0.026 0.001 TRP A 156 HIS 0.002 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 4230) covalent geometry : angle 0.53637 / 0.26 ( 5774) SS BOND : bond 0.00041 / 0.03 ( 1) SS BOND : angle 0.54776 / 0.26 ( 2) hydrogen bonds : bond 0.03477 / 2.38 ( 299) hydrogen bonds : angle 3.33420 / 2.46 ( 897) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.5940 (tpt-90) REVERT: A 7 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8022 (mp) REVERT: A 20 LEU cc_start: 0.7943 (mm) cc_final: 0.7076 (tp) REVERT: A 35 ARG cc_start: 0.7531 (mpt180) cc_final: 0.7170 (mmt-90) REVERT: A 64 GLU cc_start: 0.8815 (tt0) cc_final: 0.8077 (tp30) REVERT: A 133 THR cc_start: 0.7419 (OUTLIER) cc_final: 0.6970 (t) REVERT: A 249 MET cc_start: 0.7284 (tpt) cc_final: 0.7056 (tpt) outliers start: 22 outliers final: 18 residues processed: 81 average time/residue: 0.0492 time to fit residues: 5.4908 Evaluate side-chains 85 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 268 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.238698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.195381 restraints weight = 5762.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.198761 restraints weight = 5909.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.198901 restraints weight = 4578.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.199475 restraints weight = 3443.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.199837 restraints weight = 3040.428| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4231 Z= 0.113 Angle : 0.542 6.373 5776 Z= 0.266 Chirality : 0.034 0.135 692 Planarity : 0.004 0.030 706 Dihedral : 9.972 71.347 644 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.15 % Favored : 94.66 % Rotamer: Outliers : 5.31 % Allowed : 28.99 % Favored : 65.70 % 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: 3.17 (0.39), residues: 524 helix: 2.95 (0.26), residues: 406 sheet: None (None), residues: 0 loop : -1.20 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.011 0.001 TYR A 230 PHE 0.008 0.001 PHE A 207 TRP 0.024 0.001 TRP A 156 HIS 0.002 0.000 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 4230) covalent geometry : angle 0.54202 / 0.27 ( 5774) SS BOND : bond 0.00052 / 0.03 ( 1) SS BOND : angle 0.51295 / 0.24 ( 2) hydrogen bonds : bond 0.03514 / 2.39 ( 299) hydrogen bonds : angle 3.33181 / 2.46 ( 897) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.5956 (tpt-90) REVERT: A 7 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8028 (mp) REVERT: A 20 LEU cc_start: 0.7918 (mm) cc_final: 0.7062 (tp) REVERT: A 35 ARG cc_start: 0.7553 (mpt180) cc_final: 0.7201 (mmt-90) REVERT: A 64 GLU cc_start: 0.8799 (tt0) cc_final: 0.8073 (tp30) REVERT: A 133 THR cc_start: 0.7485 (OUTLIER) cc_final: 0.7059 (t) REVERT: A 249 MET cc_start: 0.7269 (tpt) cc_final: 0.7042 (tpt) outliers start: 22 outliers final: 19 residues processed: 80 average time/residue: 0.0490 time to fit residues: 5.4073 Evaluate side-chains 85 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.0000 chunk 38 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 0.0040 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.0000 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 overall best weight: 0.2200 ------------------------------------------------------------------------------- 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 = 0.4669 r_free = 0.4669 target = 0.240999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.198253 restraints weight = 5650.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.200732 restraints weight = 5553.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.202003 restraints weight = 4286.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.202443 restraints weight = 3270.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.202835 restraints weight = 3206.003| |-----------------------------------------------------------------------------| r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4231 Z= 0.107 Angle : 0.539 6.619 5776 Z= 0.265 Chirality : 0.034 0.140 692 Planarity : 0.004 0.029 706 Dihedral : 9.806 69.761 644 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.34 % Favored : 94.47 % Rotamer: Outliers : 4.35 % Allowed : 30.68 % Favored : 64.98 % 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: 3.23 (0.39), residues: 524 helix: 2.99 (0.26), residues: 406 sheet: None (None), residues: 0 loop : -1.18 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.012 0.001 TYR A 230 PHE 0.014 0.001 PHE B 126 TRP 0.024 0.001 TRP A 156 HIS 0.003 0.000 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 4230) covalent geometry : angle 0.53894 / 0.26 ( 5774) SS BOND : bond 0.00044 / 0.03 ( 1) SS BOND : angle 0.55884 / 0.27 ( 2) hydrogen bonds : bond 0.03333 / 2.27 ( 299) hydrogen bonds : angle 3.28358 / 2.42 ( 897) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: B 74 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.5996 (tpt-90) REVERT: A 7 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8021 (mp) REVERT: A 20 LEU cc_start: 0.7916 (mm) cc_final: 0.7279 (tp) REVERT: A 35 ARG cc_start: 0.7546 (mpt180) cc_final: 0.7218 (mmt-90) REVERT: A 64 GLU cc_start: 0.8816 (tt0) cc_final: 0.8056 (tp30) REVERT: A 133 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.7011 (t) REVERT: A 249 MET cc_start: 0.7259 (tpt) cc_final: 0.7032 (tpt) outliers start: 18 outliers final: 16 residues processed: 79 average time/residue: 0.0493 time to fit residues: 5.3662 Evaluate side-chains 81 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 0.0770 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.240089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.197615 restraints weight = 5721.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.200398 restraints weight = 5539.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.201424 restraints weight = 4256.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.202500 restraints weight = 3194.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.202633 restraints weight = 3240.840| |-----------------------------------------------------------------------------| r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4231 Z= 0.112 Angle : 0.550 6.521 5776 Z= 0.269 Chirality : 0.035 0.137 692 Planarity : 0.004 0.030 706 Dihedral : 9.853 69.366 644 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.15 % Favored : 94.66 % Rotamer: Outliers : 4.59 % Allowed : 30.68 % Favored : 64.73 % 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: 3.15 (0.39), residues: 524 helix: 2.97 (0.26), residues: 404 sheet: None (None), residues: 0 loop : -1.27 (0.65), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 144 TYR 0.012 0.001 TYR A 230 PHE 0.009 0.001 PHE A 207 TRP 0.024 0.001 TRP A 156 HIS 0.004 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 4230) covalent geometry : angle 0.54979 / 0.27 ( 5774) SS BOND : bond 0.00010 / 0.01 ( 1) SS BOND : angle 0.56359 / 0.27 ( 2) hydrogen bonds : bond 0.03412 / 2.31 ( 299) hydrogen bonds : angle 3.27843 / 2.42 ( 897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 810.79 seconds wall clock time: 14 minutes 38.76 seconds (878.76 seconds total)