Starting phenix.real_space_refine on Tue Aug 4 15:05:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9otk_70837/08_2026/9otk_70837.cif Found real_map, /net/cci-nas-00/data/ceres_data/9otk_70837/08_2026/9otk_70837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9otk_70837/08_2026/9otk_70837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9otk_70837/08_2026/9otk_70837.map" model { file = "/net/cci-nas-00/data/ceres_data/9otk_70837/08_2026/9otk_70837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9otk_70837/08_2026/9otk_70837.cif" } resolution = 3.7 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= 0.002 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 2794 2.51 5 N 682 2.21 5 O 714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4210 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2062 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 15, 'TRANS': 256} Chain: "A" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2062 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 15, 'TRANS': 256} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {' K': 1, 'LBN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' K': 3, 'LBN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 1.17, per 1000 atoms: 0.28 Number of scatterers: 4210 At special positions: 0 Unit cell: (66.8, 70.14, 98.53, 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 714 8.00 N 682 7.00 C 2794 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: 0.38 Conformation dependent library (CDL) restraints added in 159.6 milliseconds 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1012 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'B' and resid 6 through 51 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 71 through 79 removed outlier: 3.903A pdb=" N VAL B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 116 through 150 Proline residue: B 132 - end of helix Processing helix chain 'B' and resid 165 through 185 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 230 through 264 removed outlier: 3.757A pdb=" N HIS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 270 Processing helix chain 'A' and resid 6 through 51 Proline residue: A 31 - end of helix removed outlier: 3.583A pdb=" N SER A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 70 through 80 removed outlier: 4.377A pdb=" N ARG A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) 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 165 through 185 Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 230 through 263 removed outlier: 3.509A pdb=" N TYR A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 4.111A pdb=" N ILE A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 939 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: 0.51 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 722 1.33 - 1.45: 1120 1.45 - 1.57: 2450 1.57 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 4314 Sorted by residual: bond pdb=" CB PRO B 52 " pdb=" CG PRO B 52 " ideal model delta sigma weight residual 1.492 1.528 -0.036 5.00e-02 4.00e+02 5.07e-01 bond pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " ideal model delta sigma weight residual 1.529 1.539 -0.011 1.64e-02 3.72e+03 4.27e-01 bond pdb=" N ARG A 257 " pdb=" CA ARG A 257 " ideal model delta sigma weight residual 1.459 1.452 0.007 1.19e-02 7.06e+03 3.93e-01 bond pdb=" CB THR A 255 " pdb=" CG2 THR A 255 " ideal model delta sigma weight residual 1.521 1.541 -0.020 3.30e-02 9.18e+02 3.75e-01 bond pdb=" CA LEU A 268 " pdb=" C LEU A 268 " ideal model delta sigma weight residual 1.523 1.515 0.008 1.34e-02 5.57e+03 3.64e-01 ... (remaining 4309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 5746 1.51 - 3.02: 113 3.02 - 4.52: 19 4.52 - 6.03: 9 6.03 - 7.54: 3 Bond angle restraints: 5890 Sorted by residual: angle pdb=" C PHE A 209 " pdb=" N ILE A 210 " pdb=" CA ILE A 210 " ideal model delta sigma weight residual 121.97 115.70 6.27 1.80e+00 3.09e-01 1.21e+01 angle pdb=" C PHE B 209 " pdb=" N ILE B 210 " pdb=" CA ILE B 210 " ideal model delta sigma weight residual 121.97 115.79 6.18 1.80e+00 3.09e-01 1.18e+01 angle pdb=" C SER A 260 " pdb=" N ASP A 261 " pdb=" CA ASP A 261 " ideal model delta sigma weight residual 120.28 124.14 -3.86 1.44e+00 4.82e-01 7.18e+00 angle pdb=" N GLY A 264 " pdb=" CA GLY A 264 " pdb=" C GLY A 264 " ideal model delta sigma weight residual 111.78 116.20 -4.42 1.69e+00 3.50e-01 6.84e+00 angle pdb=" C ARG A 257 " pdb=" N HIS A 258 " pdb=" CA HIS A 258 " ideal model delta sigma weight residual 120.28 123.29 -3.01 1.34e+00 5.57e-01 5.04e+00 ... (remaining 5885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.12: 2409 28.12 - 56.24: 105 56.24 - 84.36: 2 84.36 - 112.48: 2 112.48 - 140.60: 5 Dihedral angle restraints: 2523 sinusoidal: 951 harmonic: 1572 Sorted by residual: dihedral pdb=" CA ILE A 210 " pdb=" C ILE A 210 " pdb=" N SER A 211 " pdb=" CA SER A 211 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ILE B 210 " pdb=" C ILE B 210 " pdb=" N SER B 211 " pdb=" CA SER B 211 " ideal model delta harmonic sigma weight residual 180.00 153.64 26.36 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" C40 LBN A 301 " pdb=" C41 LBN A 301 " pdb=" C42 LBN A 301 " pdb=" C5 LBN A 301 " ideal model delta sinusoidal sigma weight residual 117.80 -101.60 -140.60 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 2520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 427 0.027 - 0.053: 200 0.053 - 0.080: 47 0.080 - 0.106: 21 0.106 - 0.133: 9 Chirality restraints: 704 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 -2.50 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA VAL A 152 " pdb=" N VAL A 152 " pdb=" C VAL A 152 " pdb=" CB VAL A 152 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA VAL B 221 " pdb=" N VAL B 221 " pdb=" C VAL B 221 " pdb=" CB VAL B 221 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.17e-01 ... (remaining 701 not shown) Planarity restraints: 724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 51 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 52 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 164 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 165 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 257 " 0.114 9.50e-02 1.11e+02 5.11e-02 1.68e+00 pdb=" NE ARG A 257 " -0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A 257 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 257 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 257 " 0.006 2.00e-02 2.50e+03 ... (remaining 721 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.13: 3251 3.13 - 3.63: 5531 3.63 - 4.13: 6222 4.13 - 4.64: 10461 4.64 - 5.14: 12787 Nonbonded interactions: 38252 Sorted by model distance: nonbonded pdb=" O SER B 213 " pdb=" OG1 THR B 214 " model vdw 2.626 3.040 nonbonded pdb=" O SER A 213 " pdb=" OG1 THR A 214 " model vdw 2.626 3.040 nonbonded pdb=" O GLY A 130 " pdb=" OG1 THR A 133 " model vdw 2.628 3.040 nonbonded pdb=" O PHE A 209 " pdb=" CA ILE A 210 " model vdw 2.629 2.776 nonbonded pdb=" O THR B 105 " pdb=" OG1 THR B 106 " model vdw 2.631 3.040 ... (remaining 38247 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 302) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.010 Set scattering table: 0.010 Process input model: 5.560 Find NCS groups from input model: 0.050 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4315 Z= 0.120 Angle : 0.568 7.540 5892 Z= 0.282 Chirality : 0.035 0.133 704 Planarity : 0.004 0.051 724 Dihedral : 15.936 140.595 1508 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.26 % Favored : 95.56 % Rotamer: Outliers : 2.37 % Allowed : 10.43 % Favored : 87.20 % 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: 3.28 (0.39), residues: 540 helix: 2.99 (0.26), residues: 402 sheet: None (None), residues: 0 loop : -0.45 (0.61), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 257 TYR 0.009 0.001 TYR A 206 PHE 0.012 0.001 PHE B 209 TRP 0.004 0.001 TRP A 163 HIS 0.002 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 4314) covalent geometry : angle 0.56836 / 0.28 ( 5890) SS BOND : bond 0.00289 / 0.18 ( 1) SS BOND : angle 0.82440 / 0.31 ( 2) hydrogen bonds : bond 0.10504 / 7.52 ( 313) hydrogen bonds : angle 4.50399 / 3.38 ( 939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 SER cc_start: 0.9218 (m) cc_final: 0.8901 (t) REVERT: A 27 ARG cc_start: 0.7977 (tmt170) cc_final: 0.7341 (tpt170) REVERT: A 60 ASP cc_start: 0.8773 (m-30) cc_final: 0.8456 (m-30) REVERT: A 136 LEU cc_start: 0.9241 (tt) cc_final: 0.9002 (mt) REVERT: A 174 VAL cc_start: 0.9296 (t) cc_final: 0.9078 (m) REVERT: A 249 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7325 (mpt) outliers start: 10 outliers final: 5 residues processed: 142 average time/residue: 0.0454 time to fit residues: 8.8289 Evaluate side-chains 122 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 252 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 HIS B 263 HIS A 194 HIS A 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.164806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110790 restraints weight = 6630.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114728 restraints weight = 3793.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117043 restraints weight = 2867.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117884 restraints weight = 2492.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118906 restraints weight = 2343.108| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4315 Z= 0.165 Angle : 0.664 10.821 5892 Z= 0.316 Chirality : 0.038 0.122 704 Planarity : 0.004 0.034 724 Dihedral : 15.247 136.901 669 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.44 % Favored : 95.37 % Rotamer: Outliers : 4.98 % Allowed : 18.72 % Favored : 76.30 % 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: 3.29 (0.38), residues: 540 helix: 2.97 (0.26), residues: 406 sheet: None (None), residues: 0 loop : -0.44 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.012 0.002 TYR B 206 PHE 0.014 0.001 PHE A 209 TRP 0.004 0.001 TRP A 199 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 4314) covalent geometry : angle 0.66440 / 0.32 ( 5890) SS BOND : bond 0.00168 / 0.10 ( 1) SS BOND : angle 0.81858 / 0.30 ( 2) hydrogen bonds : bond 0.04112 / 2.85 ( 313) hydrogen bonds : angle 3.69044 / 2.72 ( 939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7869 (t80) REVERT: A 27 ARG cc_start: 0.8076 (tmt170) cc_final: 0.7838 (tmt170) outliers start: 21 outliers final: 15 residues processed: 128 average time/residue: 0.0424 time to fit residues: 7.6953 Evaluate side-chains 131 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 259 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 10 optimal weight: 0.0570 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 263 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.167060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112601 restraints weight = 6651.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116816 restraints weight = 3700.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119269 restraints weight = 2773.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120429 restraints weight = 2399.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120777 restraints weight = 2245.306| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4315 Z= 0.121 Angle : 0.614 9.394 5892 Z= 0.295 Chirality : 0.036 0.119 704 Planarity : 0.004 0.050 724 Dihedral : 14.569 134.914 668 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.79 % Allowed : 20.85 % Favored : 75.36 % 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: 3.34 (0.38), residues: 540 helix: 2.92 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -0.15 (0.62), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.013 0.001 TYR A 111 PHE 0.010 0.001 PHE B 209 TRP 0.004 0.001 TRP A 199 HIS 0.010 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 4314) covalent geometry : angle 0.61422 / 0.29 ( 5890) SS BOND : bond 0.00169 / 0.11 ( 1) SS BOND : angle 0.94651 / 0.35 ( 2) hydrogen bonds : bond 0.03850 / 2.66 ( 313) hydrogen bonds : angle 3.56748 / 2.63 ( 939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 SER cc_start: 0.9381 (m) cc_final: 0.9158 (t) REVERT: B 256 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7917 (t80) REVERT: A 27 ARG cc_start: 0.8096 (tmt170) cc_final: 0.7804 (tmt170) REVERT: A 249 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7501 (mpt) outliers start: 16 outliers final: 8 residues processed: 130 average time/residue: 0.0432 time to fit residues: 7.7819 Evaluate side-chains 128 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 259 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 263 HIS ** 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 = 0.4030 r_free = 0.4030 target = 0.165819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111966 restraints weight = 6612.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116018 restraints weight = 3699.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.118450 restraints weight = 2790.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119750 restraints weight = 2421.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120338 restraints weight = 2254.850| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4315 Z= 0.131 Angle : 0.614 8.691 5892 Z= 0.297 Chirality : 0.036 0.121 704 Planarity : 0.004 0.040 724 Dihedral : 13.782 132.133 667 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.27 % Allowed : 20.38 % Favored : 75.36 % 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: 3.35 (0.38), residues: 540 helix: 2.96 (0.26), residues: 406 sheet: None (None), residues: 0 loop : -0.21 (0.62), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.013 0.001 TYR A 17 PHE 0.012 0.001 PHE B 209 TRP 0.005 0.001 TRP B 199 HIS 0.011 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 4314) covalent geometry : angle 0.61421 / 0.30 ( 5890) SS BOND : bond 0.00041 / 0.03 ( 1) SS BOND : angle 0.45573 / 0.18 ( 2) hydrogen bonds : bond 0.03781 / 2.60 ( 313) hydrogen bonds : angle 3.52731 / 2.59 ( 939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 SER cc_start: 0.9385 (m) cc_final: 0.9165 (t) REVERT: B 256 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7906 (t80) REVERT: A 23 LEU cc_start: 0.9206 (mm) cc_final: 0.8818 (mm) REVERT: A 27 ARG cc_start: 0.8083 (tmt170) cc_final: 0.7804 (tmt170) REVERT: A 249 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7593 (mpt) outliers start: 18 outliers final: 11 residues processed: 130 average time/residue: 0.0466 time to fit residues: 8.3834 Evaluate side-chains 129 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.0070 chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.167896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113960 restraints weight = 6611.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118225 restraints weight = 3668.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120744 restraints weight = 2734.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122139 restraints weight = 2362.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122854 restraints weight = 2195.762| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4315 Z= 0.115 Angle : 0.608 8.392 5892 Z= 0.293 Chirality : 0.036 0.120 704 Planarity : 0.003 0.036 724 Dihedral : 13.246 127.934 667 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.79 % Allowed : 22.75 % Favored : 73.46 % 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: 3.46 (0.38), residues: 540 helix: 2.96 (0.26), residues: 408 sheet: None (None), residues: 0 loop : 0.04 (0.63), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 160 TYR 0.013 0.002 TYR B 111 PHE 0.009 0.001 PHE A 209 TRP 0.005 0.001 TRP B 91 HIS 0.007 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 4314) covalent geometry : angle 0.60832 / 0.29 ( 5890) SS BOND : bond 0.00022 / 0.01 ( 1) SS BOND : angle 0.40538 / 0.15 ( 2) hydrogen bonds : bond 0.03630 / 2.52 ( 313) hydrogen bonds : angle 3.45900 / 2.54 ( 939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 LEU cc_start: 0.8093 (tt) cc_final: 0.7462 (pp) REVERT: B 141 SER cc_start: 0.9379 (m) cc_final: 0.9159 (t) REVERT: B 256 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7962 (t80) REVERT: A 23 LEU cc_start: 0.9189 (mm) cc_final: 0.8796 (mm) REVERT: A 64 GLU cc_start: 0.8994 (tt0) cc_final: 0.8716 (mm-30) REVERT: A 249 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7593 (mpt) outliers start: 16 outliers final: 7 residues processed: 129 average time/residue: 0.0463 time to fit residues: 8.3114 Evaluate side-chains 123 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 259 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 0.0060 chunk 42 optimal weight: 0.0870 chunk 11 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.2772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.170114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117079 restraints weight = 6788.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121389 restraints weight = 3671.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123949 restraints weight = 2725.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125364 restraints weight = 2354.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125886 restraints weight = 2187.788| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4315 Z= 0.111 Angle : 0.616 8.166 5892 Z= 0.292 Chirality : 0.036 0.119 704 Planarity : 0.003 0.034 724 Dihedral : 12.549 115.498 667 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.55 % Allowed : 22.27 % Favored : 74.17 % 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: 3.55 (0.38), residues: 540 helix: 3.03 (0.26), residues: 408 sheet: None (None), residues: 0 loop : 0.07 (0.63), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.014 0.002 TYR A 17 PHE 0.007 0.001 PHE A 126 TRP 0.006 0.001 TRP B 91 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 4314) covalent geometry : angle 0.61639 / 0.29 ( 5890) SS BOND : bond 0.00005 / 0.00 ( 1) SS BOND : angle 0.38243 / 0.15 ( 2) hydrogen bonds : bond 0.03346 / 2.32 ( 313) hydrogen bonds : angle 3.37150 / 2.49 ( 939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 SER cc_start: 0.9366 (m) cc_final: 0.9128 (t) REVERT: B 256 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.8049 (t80) REVERT: A 23 LEU cc_start: 0.9182 (mm) cc_final: 0.8787 (mm) REVERT: A 249 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7619 (mpt) REVERT: A 254 GLN cc_start: 0.8973 (mt0) cc_final: 0.8713 (mt0) outliers start: 15 outliers final: 7 residues processed: 125 average time/residue: 0.0464 time to fit residues: 8.0764 Evaluate side-chains 119 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 249 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 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 = 0.4041 r_free = 0.4041 target = 0.167687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113588 restraints weight = 6621.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117684 restraints weight = 3711.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120197 restraints weight = 2772.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121169 restraints weight = 2399.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122129 restraints weight = 2252.710| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4315 Z= 0.134 Angle : 0.664 11.631 5892 Z= 0.317 Chirality : 0.038 0.143 704 Planarity : 0.004 0.033 724 Dihedral : 12.252 106.925 667 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.32 % Allowed : 23.46 % Favored : 73.22 % 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: 3.45 (0.38), residues: 540 helix: 2.89 (0.25), residues: 410 sheet: None (None), residues: 0 loop : 0.25 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.019 0.002 TYR A 111 PHE 0.011 0.001 PHE A 209 TRP 0.005 0.001 TRP B 199 HIS 0.003 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 4314) covalent geometry : angle 0.66367 / 0.32 ( 5890) SS BOND : bond 0.00037 / 0.02 ( 1) SS BOND : angle 0.30926 / 0.12 ( 2) hydrogen bonds : bond 0.03538 / 2.45 ( 313) hydrogen bonds : angle 3.46470 / 2.53 ( 939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 SER cc_start: 0.9368 (m) cc_final: 0.9147 (t) REVERT: B 256 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.8056 (t80) REVERT: A 23 LEU cc_start: 0.9186 (mm) cc_final: 0.8814 (mm) REVERT: A 60 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8777 (m-30) REVERT: A 254 GLN cc_start: 0.8944 (mt0) cc_final: 0.8706 (mt0) outliers start: 14 outliers final: 7 residues processed: 122 average time/residue: 0.0399 time to fit residues: 7.0644 Evaluate side-chains 122 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.0070 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.0270 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.168864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115844 restraints weight = 6584.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120143 restraints weight = 3603.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122626 restraints weight = 2678.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123686 restraints weight = 2311.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124663 restraints weight = 2160.062| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4315 Z= 0.122 Angle : 0.670 9.451 5892 Z= 0.318 Chirality : 0.038 0.202 704 Planarity : 0.004 0.033 724 Dihedral : 11.405 105.227 664 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.08 % Allowed : 23.46 % Favored : 73.46 % 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: 3.39 (0.38), residues: 540 helix: 2.84 (0.26), residues: 410 sheet: None (None), residues: 0 loop : 0.26 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.018 0.002 TYR A 111 PHE 0.009 0.001 PHE A 209 TRP 0.005 0.001 TRP B 91 HIS 0.003 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 4314) covalent geometry : angle 0.67026 / 0.32 ( 5890) SS BOND : bond 0.00021 / 0.01 ( 1) SS BOND : angle 0.38551 / 0.15 ( 2) hydrogen bonds : bond 0.03508 / 2.45 ( 313) hydrogen bonds : angle 3.47027 / 2.54 ( 939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 ASP cc_start: 0.8838 (m-30) cc_final: 0.8169 (p0) REVERT: B 141 SER cc_start: 0.9365 (m) cc_final: 0.9127 (t) REVERT: B 256 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8131 (t80) REVERT: A 23 LEU cc_start: 0.9184 (mm) cc_final: 0.8814 (mm) REVERT: A 254 GLN cc_start: 0.8937 (mt0) cc_final: 0.8716 (mt0) outliers start: 13 outliers final: 5 residues processed: 120 average time/residue: 0.0439 time to fit residues: 7.5832 Evaluate side-chains 117 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 259 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.169006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115885 restraints weight = 6661.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120041 restraints weight = 3641.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122641 restraints weight = 2707.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123498 restraints weight = 2324.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124666 restraints weight = 2181.410| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4315 Z= 0.127 Angle : 0.681 9.628 5892 Z= 0.328 Chirality : 0.039 0.271 704 Planarity : 0.003 0.032 724 Dihedral : 11.038 105.062 664 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.37 % Allowed : 24.88 % Favored : 72.75 % 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: 3.33 (0.38), residues: 540 helix: 2.80 (0.25), residues: 410 sheet: None (None), residues: 0 loop : 0.23 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 160 TYR 0.021 0.002 TYR A 17 PHE 0.010 0.001 PHE A 209 TRP 0.005 0.001 TRP B 91 HIS 0.003 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 4314) covalent geometry : angle 0.68076 / 0.33 ( 5890) SS BOND : bond 0.00022 / 0.01 ( 1) SS BOND : angle 0.38574 / 0.15 ( 2) hydrogen bonds : bond 0.03523 / 2.46 ( 313) hydrogen bonds : angle 3.47983 / 2.54 ( 939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 ASP cc_start: 0.8855 (m-30) cc_final: 0.8171 (p0) REVERT: B 141 SER cc_start: 0.9365 (m) cc_final: 0.9125 (t) REVERT: B 256 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.8087 (t80) REVERT: A 23 LEU cc_start: 0.9185 (mm) cc_final: 0.8810 (mm) REVERT: A 254 GLN cc_start: 0.8945 (mt0) cc_final: 0.8733 (mt0) REVERT: A 268 LEU cc_start: 0.7921 (mp) cc_final: 0.7710 (pp) outliers start: 10 outliers final: 6 residues processed: 117 average time/residue: 0.0419 time to fit residues: 7.0390 Evaluate side-chains 117 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.167398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114150 restraints weight = 6562.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118228 restraints weight = 3643.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120617 restraints weight = 2727.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121604 restraints weight = 2362.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121604 restraints weight = 2209.206| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4315 Z= 0.142 Angle : 0.707 9.508 5892 Z= 0.344 Chirality : 0.040 0.253 704 Planarity : 0.004 0.033 724 Dihedral : 10.901 104.439 664 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.90 % Allowed : 24.88 % Favored : 73.22 % 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: 3.25 (0.38), residues: 540 helix: 2.73 (0.26), residues: 410 sheet: None (None), residues: 0 loop : 0.24 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 160 TYR 0.024 0.002 TYR A 111 PHE 0.012 0.001 PHE A 209 TRP 0.004 0.001 TRP B 199 HIS 0.003 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 4314) covalent geometry : angle 0.70759 / 0.34 ( 5890) SS BOND : bond 0.00006 / 0.00 ( 1) SS BOND : angle 0.32381 / 0.12 ( 2) hydrogen bonds : bond 0.03663 / 2.54 ( 313) hydrogen bonds : angle 3.53323 / 2.57 ( 939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 ASP cc_start: 0.8848 (m-30) cc_final: 0.8209 (p0) REVERT: B 126 PHE cc_start: 0.8409 (t80) cc_final: 0.8094 (t80) REVERT: B 141 SER cc_start: 0.9371 (m) cc_final: 0.9139 (t) REVERT: B 256 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8077 (t80) REVERT: A 23 LEU cc_start: 0.9178 (mm) cc_final: 0.8806 (mm) REVERT: A 254 GLN cc_start: 0.8942 (mt0) cc_final: 0.8736 (mt0) REVERT: A 268 LEU cc_start: 0.7963 (mp) cc_final: 0.7749 (pp) outliers start: 8 outliers final: 6 residues processed: 120 average time/residue: 0.0415 time to fit residues: 7.2078 Evaluate side-chains 123 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 254 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 = 0.4051 r_free = 0.4051 target = 0.169928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113689 restraints weight = 6732.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118058 restraints weight = 3735.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120360 restraints weight = 2815.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.121213 restraints weight = 2466.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122497 restraints weight = 2328.379| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4315 Z= 0.128 Angle : 0.699 9.428 5892 Z= 0.340 Chirality : 0.039 0.255 704 Planarity : 0.003 0.033 724 Dihedral : 10.752 103.984 664 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.13 % Allowed : 25.36 % Favored : 72.51 % 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: 3.24 (0.38), residues: 540 helix: 2.74 (0.26), residues: 410 sheet: None (None), residues: 0 loop : 0.16 (0.63), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 160 TYR 0.022 0.002 TYR B 220 PHE 0.010 0.001 PHE A 209 TRP 0.005 0.001 TRP A 199 HIS 0.003 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 4314) covalent geometry : angle 0.69948 / 0.34 ( 5890) SS BOND : bond 0.00018 / 0.01 ( 1) SS BOND : angle 0.44185 / 0.18 ( 2) hydrogen bonds : bond 0.03527 / 2.45 ( 313) hydrogen bonds : angle 3.48366 / 2.54 ( 939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 918.53 seconds wall clock time: 16 minutes 25.43 seconds (985.43 seconds total)