Starting phenix.real_space_refine on Tue Aug 4 12:03:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9n_65782/08_2026/9w9n_65782.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9n_65782/08_2026/9w9n_65782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w9n_65782/08_2026/9w9n_65782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9n_65782/08_2026/9w9n_65782.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w9n_65782/08_2026/9w9n_65782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9n_65782/08_2026/9w9n_65782.map" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 1377 2.51 5 N 354 2.21 5 O 405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2139 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 713 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 713 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 713 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 0.45, per 1000 atoms: 0.21 Number of scatterers: 2139 At special positions: 0 Unit cell: (65.1, 87.42, 30.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 3 16.00 O 405 8.00 N 354 7.00 C 1377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.09 Conformation dependent library (CDL) restraints added in 47.4 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 522 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 47.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 16 removed outlier: 6.349A pdb=" N LEU A 12 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LYS C 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 14 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 6.334A pdb=" N VAL A 20 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 34 removed outlier: 6.320A pdb=" N ALA A 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL B 28 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN A 27 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL B 30 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA A 29 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL B 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS A 31 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ARG B 34 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE A 33 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.407A pdb=" N THR A 59 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLU C 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU A 61 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.860A pdb=" N GLU A 66 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL A 65 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ILE C 68 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY A 67 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 73 removed outlier: 6.259A pdb=" N GLU A 72 " --> pdb=" O ILE C 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 80 removed outlier: 6.901A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N LYS A 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N TRP C 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N TYR A 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 92 through 99 removed outlier: 6.390A pdb=" N GLU A 92 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE C 95 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 94 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA C 97 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR A 96 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP C 99 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN A 98 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 110 removed outlier: 6.881A pdb=" N TYR B 105 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR A 106 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE B 107 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA A 108 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N TYR A 105 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N ALA C 108 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 107 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N LEU C 110 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA A 109 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 118 through 122 removed outlier: 5.702A pdb=" N THR A 118 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL B 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA A 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) 37 hydrogen bonds defined for protein. 111 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: 0.17 Time building geometry restraints manager: 0.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 658 1.34 - 1.45: 293 1.45 - 1.57: 1230 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 2187 Sorted by residual: bond pdb=" CG ARG C 34 " pdb=" CD ARG C 34 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.70e-01 bond pdb=" CG ARG B 34 " pdb=" CD ARG B 34 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CG ARG A 34 " pdb=" CD ARG A 34 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 bond pdb=" CE LYS A 35 " pdb=" NZ LYS A 35 " ideal model delta sigma weight residual 1.489 1.461 0.028 3.00e-02 1.11e+03 8.41e-01 bond pdb=" CE LYS B 35 " pdb=" NZ LYS B 35 " ideal model delta sigma weight residual 1.489 1.462 0.027 3.00e-02 1.11e+03 8.35e-01 ... (remaining 2182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 2683 1.04 - 2.08: 190 2.08 - 3.11: 49 3.11 - 4.15: 33 4.15 - 5.19: 21 Bond angle restraints: 2976 Sorted by residual: angle pdb=" C PRO B 113 " pdb=" N TYR B 114 " pdb=" CA TYR B 114 " ideal model delta sigma weight residual 122.39 117.91 4.48 1.48e+00 4.57e-01 9.15e+00 angle pdb=" C PRO A 113 " pdb=" N TYR A 114 " pdb=" CA TYR A 114 " ideal model delta sigma weight residual 122.39 117.93 4.46 1.48e+00 4.57e-01 9.09e+00 angle pdb=" C PRO C 113 " pdb=" N TYR C 114 " pdb=" CA TYR C 114 " ideal model delta sigma weight residual 122.39 117.97 4.42 1.48e+00 4.57e-01 8.93e+00 angle pdb=" CA TYR B 114 " pdb=" CB TYR B 114 " pdb=" CG TYR B 114 " ideal model delta sigma weight residual 113.90 118.44 -4.54 1.80e+00 3.09e-01 6.36e+00 angle pdb=" CA TYR C 114 " pdb=" CB TYR C 114 " pdb=" CG TYR C 114 " ideal model delta sigma weight residual 113.90 118.44 -4.54 1.80e+00 3.09e-01 6.35e+00 ... (remaining 2971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 1164 16.75 - 33.50: 84 33.50 - 50.25: 45 50.25 - 67.00: 0 67.00 - 83.75: 3 Dihedral angle restraints: 1296 sinusoidal: 489 harmonic: 807 Sorted by residual: dihedral pdb=" CA ILE C 26 " pdb=" C ILE C 26 " pdb=" N ASN C 27 " pdb=" CA ASN C 27 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ILE A 26 " pdb=" C ILE A 26 " pdb=" N ASN A 27 " pdb=" CA ASN A 27 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N ASN B 27 " pdb=" CA ASN B 27 " ideal model delta harmonic sigma weight residual 180.00 158.43 21.57 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 1293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 154 0.025 - 0.049: 87 0.049 - 0.074: 50 0.074 - 0.098: 29 0.098 - 0.123: 34 Chirality restraints: 354 Sorted by residual: chirality pdb=" CA ILE B 68 " pdb=" N ILE B 68 " pdb=" C ILE B 68 " pdb=" CB ILE B 68 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 351 not shown) Planarity restraints: 366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 104 " -0.115 9.50e-02 1.11e+02 5.21e-02 2.15e+00 pdb=" NE ARG A 104 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 104 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 104 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 104 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 104 " -0.116 9.50e-02 1.11e+02 5.22e-02 2.15e+00 pdb=" NE ARG B 104 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 104 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 104 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 104 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 104 " -0.114 9.50e-02 1.11e+02 5.17e-02 2.13e+00 pdb=" NE ARG C 104 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 104 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 104 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 104 " -0.000 2.00e-02 2.50e+03 ... (remaining 363 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 423 2.80 - 3.33: 1737 3.33 - 3.85: 3931 3.85 - 4.38: 4097 4.38 - 4.90: 7873 Nonbonded interactions: 18061 Sorted by model distance: nonbonded pdb=" OH TYR A 105 " pdb=" OD2 ASP C 74 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP A 74 " pdb=" OH TYR B 105 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 114 " pdb=" OG1 THR C 119 " model vdw 2.340 3.040 nonbonded pdb=" OD1 ASP A 74 " pdb=" NZ LYS C 76 " model vdw 2.342 3.120 nonbonded pdb=" NZ LYS A 76 " pdb=" OD1 ASP B 74 " model vdw 2.351 3.120 ... (remaining 18056 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' selection = chain 'B' selection = chain 'C' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.560 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.004 0.030 2187 Z= 0.166 Angle : 0.817 5.189 2976 Z= 0.441 Chirality : 0.052 0.123 354 Planarity : 0.007 0.052 366 Dihedral : 15.042 83.746 774 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 15.38 % Favored : 84.62 % 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: -3.26 (0.40), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.003 ARG C 104 TYR 0.024 0.002 TYR B 114 PHE 0.007 0.001 PHE B 33 TRP 0.003 0.001 TRP A 79 HIS 0.001 0.000 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 ( 2187) covalent geometry : angle 0.81726 / 0.44 ( 2976) hydrogen bonds : bond 0.17132 / 11.55 ( 37) hydrogen bonds : angle 10.20603 / 7.10 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.049 Fit side-chains REVERT: A 34 ARG cc_start: 0.8428 (tpt-90) cc_final: 0.7860 (ttt180) REVERT: A 62 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7341 (mt-10) REVERT: A 104 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7807 (mtp85) REVERT: B 34 ARG cc_start: 0.8495 (tpt-90) cc_final: 0.7997 (ttt180) REVERT: B 62 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7272 (mt-10) REVERT: B 104 ARG cc_start: 0.8231 (mtt90) cc_final: 0.7845 (mtp85) REVERT: C 104 ARG cc_start: 0.8255 (mtt90) cc_final: 0.7890 (mtp85) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.5720 time to fit residues: 27.2342 Evaluate side-chains 41 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.0050 chunk 11 optimal weight: 9.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN B 98 ASN C 31 HIS C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.148901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.122501 restraints weight = 2007.443| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.58 r_work: 0.3583 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2187 Z= 0.124 Angle : 0.507 4.121 2976 Z= 0.274 Chirality : 0.050 0.130 354 Planarity : 0.003 0.023 366 Dihedral : 5.261 22.337 297 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.85 % Allowed : 14.96 % Favored : 84.19 % 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: -2.91 (0.43), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 104 TYR 0.017 0.001 TYR A 114 PHE 0.007 0.001 PHE A 95 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 2187) covalent geometry : angle 0.50670 / 0.27 ( 2976) hydrogen bonds : bond 0.02534 / 1.57 ( 37) hydrogen bonds : angle 6.31295 / 4.42 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.081 Fit side-chains REVERT: A 15 LYS cc_start: 0.8548 (tttt) cc_final: 0.8194 (ttmm) REVERT: A 34 ARG cc_start: 0.8439 (tpt-90) cc_final: 0.7783 (ttt180) REVERT: A 62 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7416 (mt-10) REVERT: A 104 ARG cc_start: 0.8395 (mtt90) cc_final: 0.8026 (mtp85) REVERT: B 15 LYS cc_start: 0.8575 (tttt) cc_final: 0.8267 (mtpm) REVERT: B 34 ARG cc_start: 0.8513 (tpt-90) cc_final: 0.8169 (ttt180) REVERT: B 62 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7372 (mt-10) REVERT: B 104 ARG cc_start: 0.8437 (mtt90) cc_final: 0.8038 (mtp85) REVERT: C 15 LYS cc_start: 0.8618 (tttt) cc_final: 0.8294 (mtpm) REVERT: C 21 ARG cc_start: 0.8466 (ttt90) cc_final: 0.8264 (ttt90) REVERT: C 63 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7338 (mm-30) REVERT: C 104 ARG cc_start: 0.8311 (mtt90) cc_final: 0.7934 (mtp85) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.6181 time to fit residues: 30.6867 Evaluate side-chains 47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.146487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119430 restraints weight = 2033.672| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.60 r_work: 0.3553 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2187 Z= 0.131 Angle : 0.496 3.494 2976 Z= 0.271 Chirality : 0.049 0.125 354 Planarity : 0.003 0.017 366 Dihedral : 5.149 22.259 297 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.71 % Allowed : 16.67 % Favored : 81.62 % 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: -2.64 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 104 TYR 0.017 0.002 TYR A 114 PHE 0.008 0.001 PHE C 87 TRP 0.004 0.001 TRP B 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 2187) covalent geometry : angle 0.49621 / 0.27 ( 2976) hydrogen bonds : bond 0.02399 / 1.52 ( 37) hydrogen bonds : angle 5.40595 / 3.79 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.083 Fit side-chains REVERT: A 34 ARG cc_start: 0.8432 (tpt-90) cc_final: 0.7812 (ttt180) REVERT: A 62 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7471 (mt-10) REVERT: A 80 LYS cc_start: 0.8836 (tttm) cc_final: 0.8486 (ttmm) REVERT: A 104 ARG cc_start: 0.8381 (mtt90) cc_final: 0.8069 (mtp85) REVERT: B 34 ARG cc_start: 0.8526 (tpt-90) cc_final: 0.7974 (ttm170) REVERT: B 62 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7399 (mt-10) REVERT: B 104 ARG cc_start: 0.8396 (mtt90) cc_final: 0.8059 (mtp85) REVERT: C 15 LYS cc_start: 0.8608 (tttt) cc_final: 0.8271 (ttmm) REVERT: C 63 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7390 (mm-30) REVERT: C 89 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7690 (mt-10) REVERT: C 104 ARG cc_start: 0.8326 (mtt90) cc_final: 0.7969 (mtp85) outliers start: 4 outliers final: 1 residues processed: 50 average time/residue: 0.8234 time to fit residues: 41.6950 Evaluate side-chains 49 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 0.0050 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.144395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.117389 restraints weight = 2001.057| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.57 r_work: 0.3523 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2187 Z= 0.159 Angle : 0.516 3.734 2976 Z= 0.283 Chirality : 0.049 0.126 354 Planarity : 0.003 0.019 366 Dihedral : 5.283 22.940 297 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.42 % Allowed : 13.68 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.019 0.002 TYR A 114 PHE 0.007 0.001 PHE C 87 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 2187) covalent geometry : angle 0.51647 / 0.28 ( 2976) hydrogen bonds : bond 0.02444 / 1.51 ( 37) hydrogen bonds : angle 5.14897 / 3.61 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.083 Fit side-chains REVERT: A 15 LYS cc_start: 0.8526 (tttt) cc_final: 0.8182 (ttmm) REVERT: A 34 ARG cc_start: 0.8433 (tpt-90) cc_final: 0.7859 (ttt180) REVERT: A 62 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7481 (mt-10) REVERT: A 80 LYS cc_start: 0.8860 (tttm) cc_final: 0.8485 (ttmm) REVERT: A 92 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: A 104 ARG cc_start: 0.8369 (mtt90) cc_final: 0.8061 (mtp85) REVERT: B 34 ARG cc_start: 0.8528 (tpt-90) cc_final: 0.8086 (ttt180) REVERT: B 62 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7433 (mt-10) REVERT: B 104 ARG cc_start: 0.8382 (mtt90) cc_final: 0.8060 (mtp85) REVERT: C 15 LYS cc_start: 0.8629 (tttt) cc_final: 0.8277 (ttmm) REVERT: C 63 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7376 (mm-30) REVERT: C 89 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7660 (mt-10) REVERT: C 104 ARG cc_start: 0.8339 (mtt90) cc_final: 0.7993 (mtp85) outliers start: 8 outliers final: 2 residues processed: 53 average time/residue: 0.8748 time to fit residues: 46.9382 Evaluate side-chains 53 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.141742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114164 restraints weight = 2010.986| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.57 r_work: 0.3474 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2187 Z= 0.211 Angle : 0.562 4.079 2976 Z= 0.306 Chirality : 0.050 0.125 354 Planarity : 0.004 0.025 366 Dihedral : 5.513 23.323 297 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.56 % Allowed : 14.10 % Favored : 83.33 % 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: -2.49 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 104 TYR 0.021 0.002 TYR A 114 PHE 0.007 0.002 PHE C 87 TRP 0.003 0.001 TRP C 79 HIS 0.003 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 ( 2187) covalent geometry : angle 0.56216 / 0.31 ( 2976) hydrogen bonds : bond 0.02711 / 1.68 ( 37) hydrogen bonds : angle 5.16445 / 3.63 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.095 Fit side-chains REVERT: A 15 LYS cc_start: 0.8544 (tttt) cc_final: 0.8208 (ttmm) REVERT: A 34 ARG cc_start: 0.8435 (tpt-90) cc_final: 0.7891 (ttt180) REVERT: A 62 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7516 (mt-10) REVERT: A 80 LYS cc_start: 0.8864 (tttm) cc_final: 0.8502 (ttmm) REVERT: A 89 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: A 104 ARG cc_start: 0.8374 (mtt90) cc_final: 0.8067 (mtp85) REVERT: B 15 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8444 (ttmm) REVERT: B 34 ARG cc_start: 0.8532 (tpt-90) cc_final: 0.8091 (ttt180) REVERT: B 62 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7486 (mt-10) REVERT: B 104 ARG cc_start: 0.8348 (mtt90) cc_final: 0.8020 (mtp85) REVERT: C 15 LYS cc_start: 0.8645 (tttt) cc_final: 0.8295 (ttmm) REVERT: C 63 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7217 (mm-30) REVERT: C 89 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: C 104 ARG cc_start: 0.8365 (mtt90) cc_final: 0.8022 (mtp85) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.9173 time to fit residues: 50.1497 Evaluate side-chains 56 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 89 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 0.0770 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.142730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.115503 restraints weight = 1976.372| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.55 r_work: 0.3493 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2187 Z= 0.186 Angle : 0.543 3.870 2976 Z= 0.296 Chirality : 0.049 0.126 354 Planarity : 0.003 0.022 366 Dihedral : 5.483 22.980 297 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.99 % Allowed : 12.82 % Favored : 84.19 % 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: -2.45 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 104 TYR 0.020 0.002 TYR A 114 PHE 0.006 0.001 PHE C 87 TRP 0.002 0.001 TRP A 79 HIS 0.003 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 2187) covalent geometry : angle 0.54335 / 0.30 ( 2976) hydrogen bonds : bond 0.02523 / 1.55 ( 37) hydrogen bonds : angle 5.11172 / 3.59 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.082 Fit side-chains REVERT: A 15 LYS cc_start: 0.8523 (tttt) cc_final: 0.8191 (ttmm) REVERT: A 34 ARG cc_start: 0.8435 (tpt-90) cc_final: 0.7890 (ttt180) REVERT: A 62 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7522 (mt-10) REVERT: A 80 LYS cc_start: 0.8861 (tttm) cc_final: 0.8502 (ttmm) REVERT: A 89 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: A 104 ARG cc_start: 0.8351 (mtt90) cc_final: 0.8054 (mtp85) REVERT: B 15 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8408 (ttmm) REVERT: B 34 ARG cc_start: 0.8536 (tpt-90) cc_final: 0.8088 (ttt180) REVERT: B 62 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7493 (mt-10) REVERT: B 104 ARG cc_start: 0.8350 (mtt90) cc_final: 0.8029 (mtp85) REVERT: C 15 LYS cc_start: 0.8641 (tttt) cc_final: 0.8299 (ttmm) REVERT: C 63 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7235 (mm-30) REVERT: C 89 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: C 104 ARG cc_start: 0.8352 (mtt90) cc_final: 0.7982 (mtp85) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 0.9268 time to fit residues: 50.6707 Evaluate side-chains 56 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 89 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 0.0570 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.4902 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.145347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.118172 restraints weight = 1962.871| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.56 r_work: 0.3537 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2187 Z= 0.141 Angle : 0.512 3.740 2976 Z= 0.279 Chirality : 0.049 0.127 354 Planarity : 0.003 0.021 366 Dihedral : 5.306 22.339 297 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.14 % Allowed : 13.25 % Favored : 84.62 % 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: -2.43 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 104 TYR 0.018 0.002 TYR A 114 PHE 0.006 0.001 PHE C 87 TRP 0.001 0.000 TRP A 79 HIS 0.002 0.000 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 2187) covalent geometry : angle 0.51222 / 0.28 ( 2976) hydrogen bonds : bond 0.02171 / 1.33 ( 37) hydrogen bonds : angle 5.03018 / 3.52 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.086 Fit side-chains REVERT: A 15 LYS cc_start: 0.8528 (tttt) cc_final: 0.8192 (ttmm) REVERT: A 34 ARG cc_start: 0.8419 (tpt-90) cc_final: 0.7883 (ttt180) REVERT: A 62 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7490 (mt-10) REVERT: A 80 LYS cc_start: 0.8841 (tttm) cc_final: 0.8542 (ttmm) REVERT: A 89 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: A 92 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: A 104 ARG cc_start: 0.8342 (mtt90) cc_final: 0.8050 (mtp85) REVERT: B 15 LYS cc_start: 0.8645 (mttt) cc_final: 0.8370 (ttmm) REVERT: B 21 ARG cc_start: 0.8430 (ttt90) cc_final: 0.8111 (mmm160) REVERT: B 34 ARG cc_start: 0.8539 (tpt-90) cc_final: 0.8088 (ttt180) REVERT: B 62 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7442 (mt-10) REVERT: B 104 ARG cc_start: 0.8328 (mtt90) cc_final: 0.8011 (mtp85) REVERT: C 15 LYS cc_start: 0.8653 (tttt) cc_final: 0.8309 (ttmm) REVERT: C 63 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7281 (mm-30) REVERT: C 89 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: C 104 ARG cc_start: 0.8317 (mtt90) cc_final: 0.7949 (mtp85) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.8896 time to fit residues: 47.7134 Evaluate side-chains 54 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 89 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.149842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.123493 restraints weight = 1994.333| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.54 r_work: 0.3612 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2187 Z= 0.100 Angle : 0.479 4.691 2976 Z= 0.258 Chirality : 0.049 0.127 354 Planarity : 0.003 0.019 366 Dihedral : 5.076 21.530 297 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.71 % Allowed : 14.10 % Favored : 84.19 % 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: -2.42 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.014 0.001 TYR A 114 PHE 0.005 0.001 PHE B 95 TRP 0.001 0.000 TRP A 79 HIS 0.001 0.000 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 2187) covalent geometry : angle 0.47902 / 0.26 ( 2976) hydrogen bonds : bond 0.01782 / 1.10 ( 37) hydrogen bonds : angle 4.92435 / 3.44 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.081 Fit side-chains REVERT: A 15 LYS cc_start: 0.8482 (tttt) cc_final: 0.8160 (ttmm) REVERT: A 34 ARG cc_start: 0.8426 (tpt-90) cc_final: 0.7788 (ttt180) REVERT: A 62 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7464 (mt-10) REVERT: A 80 LYS cc_start: 0.8812 (tttm) cc_final: 0.8513 (ttmm) REVERT: A 92 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: A 104 ARG cc_start: 0.8334 (mtt90) cc_final: 0.8055 (mtp85) REVERT: B 13 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7286 (tmm) REVERT: B 15 LYS cc_start: 0.8596 (mttt) cc_final: 0.8311 (ttmm) REVERT: B 21 ARG cc_start: 0.8198 (ttt90) cc_final: 0.7957 (mmm160) REVERT: B 34 ARG cc_start: 0.8506 (tpt-90) cc_final: 0.8077 (ttt180) REVERT: B 62 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7364 (mt-10) REVERT: B 104 ARG cc_start: 0.8298 (mtt90) cc_final: 0.7996 (mtp85) REVERT: C 63 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7292 (mm-30) REVERT: C 89 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7598 (mt-10) REVERT: C 104 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7928 (mtp85) outliers start: 4 outliers final: 1 residues processed: 52 average time/residue: 0.6317 time to fit residues: 33.3170 Evaluate side-chains 52 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.143801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.116576 restraints weight = 2012.671| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.56 r_work: 0.3509 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2187 Z= 0.162 Angle : 0.533 5.001 2976 Z= 0.288 Chirality : 0.049 0.127 354 Planarity : 0.003 0.020 366 Dihedral : 5.311 22.655 297 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.28 % Allowed : 14.10 % Favored : 84.62 % 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: -2.40 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 104 TYR 0.018 0.002 TYR A 114 PHE 0.006 0.001 PHE B 95 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 2187) covalent geometry : angle 0.53341 / 0.29 ( 2976) hydrogen bonds : bond 0.02297 / 1.42 ( 37) hydrogen bonds : angle 4.93072 / 3.45 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.048 Fit side-chains REVERT: A 15 LYS cc_start: 0.8527 (tttt) cc_final: 0.8208 (ttmm) REVERT: A 34 ARG cc_start: 0.8421 (tpt-90) cc_final: 0.7860 (ttt180) REVERT: A 62 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7505 (mt-10) REVERT: A 80 LYS cc_start: 0.8848 (tttm) cc_final: 0.8563 (ttmm) REVERT: A 92 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: A 104 ARG cc_start: 0.8348 (mtt90) cc_final: 0.8060 (mtp85) REVERT: B 15 LYS cc_start: 0.8665 (mttt) cc_final: 0.8405 (ttmm) REVERT: B 21 ARG cc_start: 0.8350 (ttt90) cc_final: 0.8028 (mmm160) REVERT: B 34 ARG cc_start: 0.8607 (tpt-90) cc_final: 0.8155 (ttt180) REVERT: B 62 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7455 (mt-10) REVERT: B 92 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: B 104 ARG cc_start: 0.8319 (mtt90) cc_final: 0.8005 (mtp85) REVERT: C 63 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7210 (mm-30) REVERT: C 89 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7710 (mt-10) REVERT: C 104 ARG cc_start: 0.8366 (mtt90) cc_final: 0.8005 (mtp85) outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 0.6331 time to fit residues: 32.6848 Evaluate side-chains 54 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 92 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.140569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.112905 restraints weight = 2092.913| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.59 r_work: 0.3456 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2187 Z= 0.235 Angle : 0.593 5.712 2976 Z= 0.320 Chirality : 0.050 0.126 354 Planarity : 0.004 0.027 366 Dihedral : 5.621 23.267 297 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.14 % Allowed : 13.25 % Favored : 84.62 % 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: -2.42 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 34 TYR 0.019 0.002 TYR A 114 PHE 0.007 0.002 PHE B 95 TRP 0.002 0.001 TRP C 79 HIS 0.003 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 ( 2187) covalent geometry : angle 0.59293 / 0.32 ( 2976) hydrogen bonds : bond 0.02784 / 1.71 ( 37) hydrogen bonds : angle 5.09802 / 3.57 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.049 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8596 (tttt) cc_final: 0.8283 (ttmm) REVERT: A 34 ARG cc_start: 0.8452 (tpt-90) cc_final: 0.7874 (ttt180) REVERT: A 62 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 80 LYS cc_start: 0.8879 (tttm) cc_final: 0.8582 (ttmm) REVERT: A 89 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: A 92 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: A 104 ARG cc_start: 0.8362 (mtt90) cc_final: 0.8073 (mtp85) REVERT: B 15 LYS cc_start: 0.8682 (mttt) cc_final: 0.8450 (ttmm) REVERT: B 34 ARG cc_start: 0.8599 (tpt-90) cc_final: 0.8108 (ttt180) REVERT: B 62 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 104 ARG cc_start: 0.8331 (mtt90) cc_final: 0.8008 (mtp85) REVERT: C 13 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7095 (tmt) REVERT: C 63 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7215 (mm-30) REVERT: C 89 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7793 (mt-10) REVERT: C 104 ARG cc_start: 0.8404 (mtt90) cc_final: 0.8040 (mtp85) outliers start: 5 outliers final: 1 residues processed: 54 average time/residue: 0.5954 time to fit residues: 32.5557 Evaluate side-chains 57 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 13 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.143967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.116207 restraints weight = 2034.432| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.62 r_work: 0.3508 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2187 Z= 0.159 Angle : 0.545 6.799 2976 Z= 0.292 Chirality : 0.049 0.126 354 Planarity : 0.003 0.023 366 Dihedral : 5.424 22.732 297 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.28 % Allowed : 14.10 % Favored : 84.62 % 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: -2.41 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.018 0.002 TYR A 114 PHE 0.006 0.001 PHE C 87 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 2187) covalent geometry : angle 0.54545 / 0.29 ( 2976) hydrogen bonds : bond 0.02283 / 1.38 ( 37) hydrogen bonds : angle 4.96462 / 3.47 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1238.33 seconds wall clock time: 21 minutes 44.49 seconds (1304.49 seconds total)