Starting phenix.real_space_refine on Thu Jul 24 03:12:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h1s_51771/07_2025/9h1s_51771.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h1s_51771/07_2025/9h1s_51771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h1s_51771/07_2025/9h1s_51771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h1s_51771/07_2025/9h1s_51771.map" model { file = "/net/cci-nas-00/data/ceres_data/9h1s_51771/07_2025/9h1s_51771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h1s_51771/07_2025/9h1s_51771.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 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 Zn 2 6.06 5 S 28 5.16 5 C 3140 2.51 5 N 882 2.21 5 O 942 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4994 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2496 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain: "B" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2496 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 43 SG CYS A 18 39.775 17.296 45.776 1.00172.16 S ATOM 179 SG CYS A 36 39.437 16.084 43.598 1.00208.25 S ATOM 286 SG CYS A 49 41.664 17.292 43.752 1.00159.54 S ATOM 2539 SG CYS B 18 88.798 19.950 32.780 1.00179.22 S ATOM 2675 SG CYS B 36 89.836 17.890 33.887 1.00210.11 S ATOM 2782 SG CYS B 49 87.570 18.854 34.806 1.00165.98 S Time building chain proxies: 6.48, per 1000 atoms: 1.30 Number of scatterers: 4994 At special positions: 0 Unit cell: (129.6, 59.4, 78.3, 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) Zn 2 29.99 S 28 16.00 O 942 8.00 N 882 7.00 C 3140 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: 1.95 Conformation dependent library (CDL) restraints added in 627.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 49 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 52 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 18 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 36 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 52 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 18 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 49 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 36 " Number of angles added : 6 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 37.5% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 49 through 58 Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 124 through 136 Processing helix chain 'A' and resid 144 through 164 Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 201 through 212 Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.995A pdb=" N TYR B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 164 Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 201 through 212 Processing helix chain 'B' and resid 278 through 285 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 179 removed outlier: 6.359A pdb=" N TYR A 216 " --> pdb=" O GLN A 302 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE A 304 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN A 218 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 290 removed outlier: 6.684A pdb=" N GLU A 289 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 96 removed outlier: 6.450A pdb=" N LEU B 239 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 176 through 179 removed outlier: 6.350A pdb=" N TYR B 216 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE B 304 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN B 218 " --> pdb=" O ILE B 304 " (cutoff:3.500A) 178 hydrogen bonds defined for protein. 462 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: 1.31 Time building geometry restraints manager: 1.56 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: 1480 1.33 - 1.46: 1366 1.46 - 1.59: 2210 1.59 - 1.72: 0 1.72 - 1.85: 40 Bond restraints: 5096 Sorted by residual: bond pdb=" CA PHE A 67 " pdb=" C PHE A 67 " ideal model delta sigma weight residual 1.524 1.480 0.043 1.25e-02 6.40e+03 1.20e+01 bond pdb=" CA ILE A 93 " pdb=" C ILE A 93 " ideal model delta sigma weight residual 1.527 1.499 0.028 9.70e-03 1.06e+04 8.44e+00 bond pdb=" N VAL A 243 " pdb=" CA VAL A 243 " ideal model delta sigma weight residual 1.460 1.438 0.022 7.50e-03 1.78e+04 8.25e+00 bond pdb=" CA GLN A 218 " pdb=" C GLN A 218 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.23e-02 6.61e+03 8.05e+00 bond pdb=" CA ILE A 219 " pdb=" C ILE A 219 " ideal model delta sigma weight residual 1.523 1.486 0.036 1.28e-02 6.10e+03 7.99e+00 ... (remaining 5091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 5957 2.00 - 3.99: 796 3.99 - 5.99: 114 5.99 - 7.98: 25 7.98 - 9.98: 14 Bond angle restraints: 6906 Sorted by residual: angle pdb=" C GLY A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta sigma weight residual 119.90 128.92 -9.02 1.02e+00 9.61e-01 7.82e+01 angle pdb=" C SER B 37 " pdb=" N PRO B 38 " pdb=" CA PRO B 38 " ideal model delta sigma weight residual 119.47 129.45 -9.98 1.16e+00 7.43e-01 7.40e+01 angle pdb=" C VAL A 295 " pdb=" N PRO A 296 " pdb=" CA PRO A 296 " ideal model delta sigma weight residual 119.92 128.95 -9.03 1.07e+00 8.73e-01 7.13e+01 angle pdb=" C ASN B 164 " pdb=" N PRO B 165 " pdb=" CA PRO B 165 " ideal model delta sigma weight residual 119.87 128.53 -8.66 1.04e+00 9.25e-01 6.94e+01 angle pdb=" C GLY B 246 " pdb=" N PRO B 247 " pdb=" CA PRO B 247 " ideal model delta sigma weight residual 120.31 128.22 -7.91 9.80e-01 1.04e+00 6.51e+01 ... (remaining 6901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 2980 16.46 - 32.92: 78 32.92 - 49.38: 24 49.38 - 65.84: 6 65.84 - 82.30: 4 Dihedral angle restraints: 3092 sinusoidal: 1272 harmonic: 1820 Sorted by residual: dihedral pdb=" C ASN B 228 " pdb=" N ASN B 228 " pdb=" CA ASN B 228 " pdb=" CB ASN B 228 " ideal model delta harmonic sigma weight residual -122.60 -130.46 7.86 0 2.50e+00 1.60e-01 9.89e+00 dihedral pdb=" CB GLU B 139 " pdb=" CG GLU B 139 " pdb=" CD GLU B 139 " pdb=" OE1 GLU B 139 " ideal model delta sinusoidal sigma weight residual 0.00 -78.95 78.95 1 3.00e+01 1.11e-03 8.62e+00 dihedral pdb=" CB GLU A 87 " pdb=" CG GLU A 87 " pdb=" CD GLU A 87 " pdb=" OE1 GLU A 87 " ideal model delta sinusoidal sigma weight residual 0.00 70.88 -70.88 1 3.00e+01 1.11e-03 7.17e+00 ... (remaining 3089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 509 0.073 - 0.147: 219 0.147 - 0.220: 29 0.220 - 0.294: 0 0.294 - 0.367: 1 Chirality restraints: 758 Sorted by residual: chirality pdb=" CA ASN B 228 " pdb=" N ASN B 228 " pdb=" C ASN B 228 " pdb=" CB ASN B 228 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA ASN A 100 " pdb=" N ASN A 100 " pdb=" C ASN A 100 " pdb=" CB ASN A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASN B 100 " pdb=" N ASN B 100 " pdb=" C ASN B 100 " pdb=" CB ASN B 100 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 755 not shown) Planarity restraints: 918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 301 " -0.035 2.00e-02 2.50e+03 1.82e-02 6.64e+00 pdb=" CG TYR A 301 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 301 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 301 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 301 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 301 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 301 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 301 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 52 " -0.025 2.00e-02 2.50e+03 1.93e-02 5.59e+00 pdb=" CG HIS A 52 " 0.024 2.00e-02 2.50e+03 pdb=" ND1 HIS A 52 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS A 52 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS A 52 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 52 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 200 " 0.029 2.00e-02 2.50e+03 1.63e-02 5.29e+00 pdb=" CG TYR B 200 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 200 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 200 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 200 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 200 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 200 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 200 " 0.026 2.00e-02 2.50e+03 ... (remaining 915 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1425 2.80 - 3.32: 4908 3.32 - 3.85: 8719 3.85 - 4.37: 10280 4.37 - 4.90: 16679 Nonbonded interactions: 42011 Sorted by model distance: nonbonded pdb=" N GLU B 87 " pdb=" OE1 GLU B 87 " model vdw 2.272 3.120 nonbonded pdb=" N GLU A 307 " pdb=" OE1 GLU A 307 " model vdw 2.311 3.120 nonbonded pdb=" N GLN B 102 " pdb=" OE1 GLN B 102 " model vdw 2.374 3.120 nonbonded pdb=" C ASP B 245 " pdb=" OD1 ASP B 245 " model vdw 2.457 3.270 nonbonded pdb=" OG SER A 261 " pdb=" NE2 GLN A 262 " model vdw 2.470 3.120 ... (remaining 42006 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' 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 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: 69.680 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.660 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.023 0.654 5104 Z= 1.076 Angle : 1.637 31.857 6912 Z= 1.064 Chirality : 0.073 0.367 758 Planarity : 0.006 0.036 918 Dihedral : 9.904 82.302 1912 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.31), residues: 612 helix: -0.57 (0.34), residues: 182 sheet: -2.43 (0.70), residues: 40 loop : -0.58 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.009 TRP A 46 HIS 0.013 0.003 HIS B 52 PHE 0.019 0.004 PHE B 310 TYR 0.035 0.007 TYR A 301 ARG 0.006 0.001 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.14570 ( 178) hydrogen bonds : angle 8.13432 ( 462) metal coordination : bond 0.45643 ( 8) metal coordination : angle 23.66946 ( 6) covalent geometry : bond 0.01411 ( 5096) covalent geometry : angle 1.48218 ( 6906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ILE cc_start: 0.8179 (mt) cc_final: 0.7727 (mt) REVERT: A 157 LYS cc_start: 0.9365 (mmmt) cc_final: 0.9109 (tppp) REVERT: A 219 ILE cc_start: 0.8882 (mt) cc_final: 0.8412 (mt) REVERT: A 223 GLU cc_start: 0.8468 (tt0) cc_final: 0.7954 (tm-30) REVERT: A 236 GLU cc_start: 0.9489 (pm20) cc_final: 0.9270 (pm20) REVERT: A 257 ASP cc_start: 0.8922 (p0) cc_final: 0.8563 (p0) REVERT: B 75 LYS cc_start: 0.8438 (mttt) cc_final: 0.8059 (mttt) REVERT: B 110 MET cc_start: 0.8805 (ptp) cc_final: 0.8169 (ptt) REVERT: B 114 GLU cc_start: 0.8053 (pt0) cc_final: 0.7708 (tt0) REVERT: B 150 HIS cc_start: 0.8621 (t70) cc_final: 0.8339 (m90) REVERT: B 157 LYS cc_start: 0.9324 (mmmt) cc_final: 0.9076 (mmtm) REVERT: B 215 GLU cc_start: 0.8311 (mp0) cc_final: 0.7942 (mp0) REVERT: B 218 GLN cc_start: 0.8234 (tt0) cc_final: 0.7622 (tm-30) REVERT: B 219 ILE cc_start: 0.8662 (mt) cc_final: 0.8448 (tt) REVERT: B 223 GLU cc_start: 0.8585 (tt0) cc_final: 0.8114 (tm-30) REVERT: B 236 GLU cc_start: 0.9424 (pm20) cc_final: 0.9203 (pm20) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 2.0884 time to fit residues: 310.5881 Evaluate side-chains 72 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.071532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.056939 restraints weight = 12811.095| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.20 r_work: 0.2889 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5104 Z= 0.193 Angle : 0.684 7.604 6912 Z= 0.361 Chirality : 0.047 0.154 758 Planarity : 0.005 0.035 918 Dihedral : 4.801 19.760 688 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.61 % Allowed : 10.57 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.33), residues: 612 helix: 0.49 (0.37), residues: 196 sheet: -2.28 (0.81), residues: 40 loop : -0.21 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 46 HIS 0.006 0.002 HIS B 81 PHE 0.016 0.002 PHE A 226 TYR 0.011 0.001 TYR A 32 ARG 0.007 0.001 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 178) hydrogen bonds : angle 6.04901 ( 462) metal coordination : bond 0.01906 ( 8) metal coordination : angle 5.14329 ( 6) covalent geometry : bond 0.00425 ( 5096) covalent geometry : angle 0.66737 ( 6906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.8786 (mp0) cc_final: 0.8295 (mp0) REVERT: A 114 GLU cc_start: 0.8240 (tt0) cc_final: 0.8038 (tt0) REVERT: A 184 ASN cc_start: 0.8412 (m-40) cc_final: 0.7984 (t0) REVERT: A 218 GLN cc_start: 0.8188 (tt0) cc_final: 0.7202 (tm130) REVERT: A 235 ASP cc_start: 0.9072 (p0) cc_final: 0.8781 (p0) REVERT: A 236 GLU cc_start: 0.9564 (pm20) cc_final: 0.9345 (pm20) REVERT: A 248 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7956 (tp30) REVERT: A 257 ASP cc_start: 0.8973 (p0) cc_final: 0.8743 (p0) REVERT: B 75 LYS cc_start: 0.8632 (mttt) cc_final: 0.8386 (mtmm) REVERT: B 110 MET cc_start: 0.8731 (ptp) cc_final: 0.8190 (ptt) REVERT: B 114 GLU cc_start: 0.7866 (pt0) cc_final: 0.7478 (pt0) REVERT: B 135 LEU cc_start: 0.9597 (mm) cc_final: 0.9278 (tt) REVERT: B 136 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8047 (ptpp) REVERT: B 150 HIS cc_start: 0.8919 (t70) cc_final: 0.8508 (m90) REVERT: B 218 GLN cc_start: 0.8312 (tt0) cc_final: 0.7825 (tm-30) REVERT: B 236 GLU cc_start: 0.9504 (pm20) cc_final: 0.9258 (pm20) REVERT: B 257 ASP cc_start: 0.9083 (m-30) cc_final: 0.8501 (p0) REVERT: B 305 ASN cc_start: 0.8536 (t0) cc_final: 0.8003 (p0) outliers start: 9 outliers final: 3 residues processed: 106 average time/residue: 2.1096 time to fit residues: 232.4685 Evaluate side-chains 77 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 88 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.058520 restraints weight = 12736.055| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 4.16 r_work: 0.2921 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5104 Z= 0.134 Angle : 0.603 8.092 6912 Z= 0.319 Chirality : 0.045 0.147 758 Planarity : 0.004 0.030 918 Dihedral : 4.485 20.337 688 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.43 % Allowed : 13.26 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.34), residues: 612 helix: 1.17 (0.39), residues: 184 sheet: -2.01 (0.90), residues: 32 loop : -0.24 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 46 HIS 0.004 0.001 HIS B 42 PHE 0.014 0.001 PHE B 74 TYR 0.010 0.001 TYR A 216 ARG 0.007 0.000 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 178) hydrogen bonds : angle 5.71120 ( 462) metal coordination : bond 0.00796 ( 8) metal coordination : angle 3.19365 ( 6) covalent geometry : bond 0.00301 ( 5096) covalent geometry : angle 0.59616 ( 6906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8806 (mtm) cc_final: 0.8176 (mmm) REVERT: A 73 GLN cc_start: 0.7850 (pp30) cc_final: 0.7380 (pm20) REVERT: A 114 GLU cc_start: 0.8340 (tt0) cc_final: 0.8050 (tt0) REVERT: A 184 ASN cc_start: 0.8475 (m-40) cc_final: 0.8054 (t0) REVERT: A 218 GLN cc_start: 0.8125 (tt0) cc_final: 0.7306 (tm130) REVERT: A 235 ASP cc_start: 0.9112 (p0) cc_final: 0.8818 (p0) REVERT: A 248 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7839 (tp30) REVERT: A 279 ARG cc_start: 0.9022 (ttp-110) cc_final: 0.8706 (ttm110) REVERT: A 283 ARG cc_start: 0.8843 (ttp-110) cc_final: 0.8431 (ptp-110) REVERT: B 59 MET cc_start: 0.9202 (mtt) cc_final: 0.8788 (mpt) REVERT: B 70 ASP cc_start: 0.8648 (t0) cc_final: 0.8243 (p0) REVERT: B 88 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7881 (mpt-90) REVERT: B 110 MET cc_start: 0.8664 (ptp) cc_final: 0.7972 (ptt) REVERT: B 114 GLU cc_start: 0.8030 (pt0) cc_final: 0.7564 (pt0) REVERT: B 135 LEU cc_start: 0.9509 (mm) cc_final: 0.9066 (pp) REVERT: B 218 GLN cc_start: 0.8282 (tt0) cc_final: 0.7908 (tm-30) REVERT: B 235 ASP cc_start: 0.8997 (p0) cc_final: 0.8794 (p0) REVERT: B 236 GLU cc_start: 0.9526 (pm20) cc_final: 0.9251 (pm20) REVERT: B 257 ASP cc_start: 0.8965 (m-30) cc_final: 0.8501 (p0) REVERT: B 305 ASN cc_start: 0.8494 (t0) cc_final: 0.8103 (p0) outliers start: 8 outliers final: 1 residues processed: 97 average time/residue: 1.4651 time to fit residues: 148.4126 Evaluate side-chains 71 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 88 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 31 optimal weight: 0.1980 chunk 3 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 HIS ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.057997 restraints weight = 12883.340| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 4.30 r_work: 0.2911 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5104 Z= 0.133 Angle : 0.596 7.978 6912 Z= 0.309 Chirality : 0.045 0.151 758 Planarity : 0.004 0.034 918 Dihedral : 4.295 18.222 688 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.43 % Allowed : 16.31 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.34), residues: 612 helix: 0.96 (0.38), residues: 196 sheet: -2.18 (0.85), residues: 36 loop : -0.22 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 46 HIS 0.004 0.002 HIS B 42 PHE 0.020 0.001 PHE A 226 TYR 0.008 0.001 TYR B 32 ARG 0.008 0.000 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 178) hydrogen bonds : angle 5.62763 ( 462) metal coordination : bond 0.00953 ( 8) metal coordination : angle 2.63880 ( 6) covalent geometry : bond 0.00303 ( 5096) covalent geometry : angle 0.59069 ( 6906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8737 (mtm) cc_final: 0.8241 (mmm) REVERT: A 110 MET cc_start: 0.8761 (ptp) cc_final: 0.7507 (ptt) REVERT: A 114 GLU cc_start: 0.8460 (tt0) cc_final: 0.8042 (tt0) REVERT: A 184 ASN cc_start: 0.8560 (m-40) cc_final: 0.8145 (t0) REVERT: A 235 ASP cc_start: 0.9137 (p0) cc_final: 0.8932 (p0) REVERT: A 236 GLU cc_start: 0.9291 (pm20) cc_final: 0.8923 (pm20) REVERT: A 248 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7944 (tp30) REVERT: A 279 ARG cc_start: 0.9196 (ttp-110) cc_final: 0.8624 (ttp-110) REVERT: A 283 ARG cc_start: 0.8877 (ttp-110) cc_final: 0.8620 (ptp-110) REVERT: B 70 ASP cc_start: 0.8597 (t0) cc_final: 0.8184 (p0) REVERT: B 114 GLU cc_start: 0.7981 (pt0) cc_final: 0.7744 (pt0) REVERT: B 135 LEU cc_start: 0.9487 (mm) cc_final: 0.9053 (pp) REVERT: B 136 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8182 (mtmm) REVERT: B 218 GLN cc_start: 0.8327 (tt0) cc_final: 0.7971 (tm-30) REVERT: B 236 GLU cc_start: 0.9512 (pm20) cc_final: 0.9253 (pm20) REVERT: B 253 ILE cc_start: 0.8883 (mm) cc_final: 0.8501 (pp) outliers start: 8 outliers final: 4 residues processed: 87 average time/residue: 1.9978 time to fit residues: 179.7681 Evaluate side-chains 75 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 88 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 HIS B 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.058670 restraints weight = 12796.880| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 4.28 r_work: 0.2925 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5104 Z= 0.130 Angle : 0.607 6.851 6912 Z= 0.314 Chirality : 0.045 0.154 758 Planarity : 0.004 0.037 918 Dihedral : 4.177 17.436 688 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.61 % Allowed : 16.49 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.34), residues: 612 helix: 1.02 (0.39), residues: 196 sheet: -2.44 (0.82), residues: 36 loop : -0.28 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 46 HIS 0.005 0.001 HIS B 81 PHE 0.012 0.001 PHE A 226 TYR 0.009 0.001 TYR B 32 ARG 0.009 0.000 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 178) hydrogen bonds : angle 5.51218 ( 462) metal coordination : bond 0.00780 ( 8) metal coordination : angle 2.24359 ( 6) covalent geometry : bond 0.00299 ( 5096) covalent geometry : angle 0.60384 ( 6906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8481 (t0) cc_final: 0.8181 (t0) REVERT: A 114 GLU cc_start: 0.8487 (tt0) cc_final: 0.8145 (tt0) REVERT: A 184 ASN cc_start: 0.8563 (m-40) cc_final: 0.8150 (t0) REVERT: A 218 GLN cc_start: 0.8188 (tt0) cc_final: 0.7262 (tm130) REVERT: A 235 ASP cc_start: 0.9167 (p0) cc_final: 0.8862 (p0) REVERT: A 236 GLU cc_start: 0.9332 (pm20) cc_final: 0.9000 (pm20) REVERT: A 248 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7749 (tp30) REVERT: A 279 ARG cc_start: 0.9180 (ttp-110) cc_final: 0.8484 (ttp-110) REVERT: A 283 ARG cc_start: 0.8932 (ttp-110) cc_final: 0.8614 (ptp-110) REVERT: B 70 ASP cc_start: 0.8653 (t0) cc_final: 0.8135 (p0) REVERT: B 75 LYS cc_start: 0.8813 (mttt) cc_final: 0.8516 (mttt) REVERT: B 110 MET cc_start: 0.8919 (ptt) cc_final: 0.8636 (ptt) REVERT: B 114 GLU cc_start: 0.8253 (pt0) cc_final: 0.7754 (pt0) REVERT: B 135 LEU cc_start: 0.9479 (mm) cc_final: 0.9041 (pp) REVERT: B 150 HIS cc_start: 0.7948 (t70) cc_final: 0.7485 (m90) REVERT: B 194 ASP cc_start: 0.9239 (m-30) cc_final: 0.9015 (m-30) REVERT: B 218 GLN cc_start: 0.8289 (tt0) cc_final: 0.7885 (tm-30) REVERT: B 236 GLU cc_start: 0.9525 (pm20) cc_final: 0.9226 (pm20) REVERT: B 253 ILE cc_start: 0.8960 (mm) cc_final: 0.8643 (pp) REVERT: B 310 PHE cc_start: 0.9338 (t80) cc_final: 0.9121 (t80) outliers start: 9 outliers final: 4 residues processed: 92 average time/residue: 2.0023 time to fit residues: 190.8702 Evaluate side-chains 75 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 88 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 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 = 0.3317 r_free = 0.3317 target = 0.070547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.056011 restraints weight = 12961.531| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.24 r_work: 0.2870 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5104 Z= 0.212 Angle : 0.659 7.651 6912 Z= 0.340 Chirality : 0.046 0.142 758 Planarity : 0.004 0.039 918 Dihedral : 4.462 18.278 688 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.15 % Allowed : 17.56 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.34), residues: 612 helix: 0.83 (0.39), residues: 196 sheet: -2.95 (0.78), residues: 36 loop : -0.43 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 46 HIS 0.005 0.002 HIS B 81 PHE 0.014 0.002 PHE A 226 TYR 0.011 0.002 TYR A 200 ARG 0.010 0.001 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 178) hydrogen bonds : angle 5.69110 ( 462) metal coordination : bond 0.02308 ( 8) metal coordination : angle 3.19846 ( 6) covalent geometry : bond 0.00477 ( 5096) covalent geometry : angle 0.65265 ( 6906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8741 (t0) cc_final: 0.8430 (t0) REVERT: A 87 GLU cc_start: 0.8942 (mp0) cc_final: 0.8270 (mp0) REVERT: A 102 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8854 (pm20) REVERT: A 110 MET cc_start: 0.8732 (ptp) cc_final: 0.8193 (ptt) REVERT: A 184 ASN cc_start: 0.8666 (m-40) cc_final: 0.8269 (t0) REVERT: A 235 ASP cc_start: 0.9069 (p0) cc_final: 0.8691 (p0) REVERT: A 236 GLU cc_start: 0.9370 (pm20) cc_final: 0.9163 (pm20) REVERT: A 248 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: A 279 ARG cc_start: 0.9161 (ttp-110) cc_final: 0.8534 (ttp-110) REVERT: A 283 ARG cc_start: 0.8944 (ttp-110) cc_final: 0.8598 (ptp-110) REVERT: A 318 ARG cc_start: 0.9457 (OUTLIER) cc_final: 0.9198 (mtp85) REVERT: B 59 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8523 (mpt) REVERT: B 70 ASP cc_start: 0.8682 (t0) cc_final: 0.8159 (p0) REVERT: B 73 GLN cc_start: 0.8761 (mp10) cc_final: 0.8530 (mp10) REVERT: B 75 LYS cc_start: 0.8853 (mttt) cc_final: 0.8534 (mttt) REVERT: B 88 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8289 (mpt-90) REVERT: B 114 GLU cc_start: 0.8171 (pt0) cc_final: 0.7638 (pt0) REVERT: B 150 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.7523 (m90) REVERT: B 215 GLU cc_start: 0.8352 (mp0) cc_final: 0.7722 (mp0) REVERT: B 218 GLN cc_start: 0.8322 (tt0) cc_final: 0.7937 (tm-30) REVERT: B 236 GLU cc_start: 0.9522 (pm20) cc_final: 0.9298 (pm20) REVERT: B 253 ILE cc_start: 0.9017 (mm) cc_final: 0.8569 (pp) REVERT: B 283 ARG cc_start: 0.9007 (mtm-85) cc_final: 0.8806 (mtm-85) outliers start: 12 outliers final: 1 residues processed: 86 average time/residue: 3.1521 time to fit residues: 280.1970 Evaluate side-chains 80 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 150 HIS Chi-restraints excluded: chain B residue 204 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 49 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 27 optimal weight: 0.0970 chunk 22 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 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 = 0.3331 r_free = 0.3331 target = 0.071498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.056969 restraints weight = 12853.391| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.22 r_work: 0.2892 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5104 Z= 0.156 Angle : 0.635 7.746 6912 Z= 0.327 Chirality : 0.046 0.142 758 Planarity : 0.004 0.049 918 Dihedral : 4.372 20.382 688 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.61 % Allowed : 18.64 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.34), residues: 612 helix: 0.88 (0.39), residues: 196 sheet: -2.65 (0.79), residues: 36 loop : -0.41 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 46 HIS 0.004 0.001 HIS B 81 PHE 0.010 0.001 PHE A 226 TYR 0.025 0.001 TYR B 32 ARG 0.011 0.001 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 178) hydrogen bonds : angle 5.59675 ( 462) metal coordination : bond 0.01333 ( 8) metal coordination : angle 2.39608 ( 6) covalent geometry : bond 0.00358 ( 5096) covalent geometry : angle 0.63164 ( 6906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8720 (t0) cc_final: 0.8415 (t0) REVERT: A 62 MET cc_start: 0.8902 (mtp) cc_final: 0.8647 (mtp) REVERT: A 86 LYS cc_start: 0.9476 (mmmm) cc_final: 0.9077 (mmmm) REVERT: A 87 GLU cc_start: 0.8939 (mp0) cc_final: 0.8319 (mp0) REVERT: A 110 MET cc_start: 0.8851 (ptp) cc_final: 0.8052 (ptt) REVERT: A 114 GLU cc_start: 0.8436 (tt0) cc_final: 0.8203 (tt0) REVERT: A 184 ASN cc_start: 0.8655 (m-40) cc_final: 0.8251 (t0) REVERT: A 235 ASP cc_start: 0.9063 (p0) cc_final: 0.8685 (p0) REVERT: A 236 GLU cc_start: 0.9379 (pm20) cc_final: 0.9123 (pm20) REVERT: A 248 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: A 279 ARG cc_start: 0.9159 (ttp-110) cc_final: 0.8546 (ttp-110) REVERT: A 283 ARG cc_start: 0.9014 (ttp-110) cc_final: 0.8630 (ptp-110) REVERT: A 318 ARG cc_start: 0.9482 (OUTLIER) cc_final: 0.9170 (mtp85) REVERT: B 59 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8482 (mpt) REVERT: B 70 ASP cc_start: 0.8652 (t0) cc_final: 0.8114 (p0) REVERT: B 73 GLN cc_start: 0.8740 (mp10) cc_final: 0.8517 (mp10) REVERT: B 75 LYS cc_start: 0.8780 (mttt) cc_final: 0.8579 (mtmt) REVERT: B 114 GLU cc_start: 0.8227 (pt0) cc_final: 0.7633 (pt0) REVERT: B 135 LEU cc_start: 0.9514 (mm) cc_final: 0.9035 (pp) REVERT: B 150 HIS cc_start: 0.7687 (t70) cc_final: 0.7464 (m90) REVERT: B 194 ASP cc_start: 0.9240 (m-30) cc_final: 0.8974 (m-30) REVERT: B 215 GLU cc_start: 0.8336 (mp0) cc_final: 0.7776 (mp0) REVERT: B 218 GLN cc_start: 0.8310 (tt0) cc_final: 0.7921 (tm-30) REVERT: B 236 GLU cc_start: 0.9516 (pm20) cc_final: 0.9220 (pm20) REVERT: B 253 ILE cc_start: 0.9039 (mm) cc_final: 0.8561 (pp) REVERT: B 290 GLU cc_start: 0.9266 (tt0) cc_final: 0.8502 (tm-30) REVERT: B 316 ILE cc_start: 0.9462 (mt) cc_final: 0.9255 (mp) outliers start: 9 outliers final: 4 residues processed: 89 average time/residue: 2.7561 time to fit residues: 254.2386 Evaluate side-chains 84 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 88 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 2 optimal weight: 0.0970 chunk 9 optimal weight: 0.0770 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.073867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.059264 restraints weight = 12902.416| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.26 r_work: 0.2936 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5104 Z= 0.114 Angle : 0.656 10.806 6912 Z= 0.331 Chirality : 0.045 0.141 758 Planarity : 0.004 0.049 918 Dihedral : 4.162 20.220 688 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.72 % Allowed : 19.89 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.34), residues: 612 helix: 0.99 (0.40), residues: 196 sheet: -2.55 (0.80), residues: 36 loop : -0.33 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 46 HIS 0.004 0.001 HIS B 119 PHE 0.008 0.001 PHE B 226 TYR 0.009 0.001 TYR B 153 ARG 0.012 0.001 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 178) hydrogen bonds : angle 5.40355 ( 462) metal coordination : bond 0.00312 ( 8) metal coordination : angle 1.58882 ( 6) covalent geometry : bond 0.00271 ( 5096) covalent geometry : angle 0.65511 ( 6906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8545 (t0) cc_final: 0.8241 (t0) REVERT: A 86 LYS cc_start: 0.9399 (mmmm) cc_final: 0.9024 (mmmm) REVERT: A 87 GLU cc_start: 0.8922 (mp0) cc_final: 0.8284 (mp0) REVERT: A 110 MET cc_start: 0.8724 (ptp) cc_final: 0.7810 (ptt) REVERT: A 114 GLU cc_start: 0.8425 (tt0) cc_final: 0.7990 (tt0) REVERT: A 184 ASN cc_start: 0.8630 (m-40) cc_final: 0.8217 (t0) REVERT: A 235 ASP cc_start: 0.9093 (p0) cc_final: 0.8799 (p0) REVERT: A 236 GLU cc_start: 0.9425 (pm20) cc_final: 0.9183 (pm20) REVERT: A 248 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: A 318 ARG cc_start: 0.9481 (OUTLIER) cc_final: 0.9044 (mtp85) REVERT: B 59 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8440 (mpt) REVERT: B 70 ASP cc_start: 0.8558 (t0) cc_final: 0.8227 (p0) REVERT: B 114 GLU cc_start: 0.8327 (pt0) cc_final: 0.7789 (pt0) REVERT: B 136 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8228 (ptpp) REVERT: B 150 HIS cc_start: 0.7645 (t70) cc_final: 0.7320 (m90) REVERT: B 194 ASP cc_start: 0.9189 (m-30) cc_final: 0.8947 (m-30) REVERT: B 210 ARG cc_start: 0.9320 (tpp-160) cc_final: 0.9085 (tpp-160) REVERT: B 215 GLU cc_start: 0.8396 (mp0) cc_final: 0.8023 (mp0) REVERT: B 218 GLN cc_start: 0.8268 (tt0) cc_final: 0.7848 (tm-30) REVERT: B 236 GLU cc_start: 0.9492 (pm20) cc_final: 0.9213 (pm20) REVERT: B 253 ILE cc_start: 0.8937 (mm) cc_final: 0.8396 (pp) REVERT: B 259 MET cc_start: 0.7089 (mmm) cc_final: 0.6787 (mmp) REVERT: B 283 ARG cc_start: 0.8960 (mtm-85) cc_final: 0.8526 (ptp-110) REVERT: B 290 GLU cc_start: 0.8881 (tt0) cc_final: 0.8514 (tp30) REVERT: B 316 ILE cc_start: 0.9449 (mt) cc_final: 0.9226 (mp) outliers start: 4 outliers final: 1 residues processed: 90 average time/residue: 1.4757 time to fit residues: 137.3164 Evaluate side-chains 82 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 81 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.058070 restraints weight = 12902.165| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 4.30 r_work: 0.2916 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5104 Z= 0.148 Angle : 0.714 9.812 6912 Z= 0.359 Chirality : 0.045 0.150 758 Planarity : 0.005 0.057 918 Dihedral : 4.283 18.841 688 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.25 % Allowed : 20.43 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.34), residues: 612 helix: 0.85 (0.39), residues: 196 sheet: -2.53 (0.80), residues: 36 loop : -0.34 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 46 HIS 0.003 0.001 HIS B 119 PHE 0.009 0.001 PHE B 226 TYR 0.022 0.001 TYR B 32 ARG 0.013 0.001 ARG B 17 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 178) hydrogen bonds : angle 5.44786 ( 462) metal coordination : bond 0.01051 ( 8) metal coordination : angle 2.05346 ( 6) covalent geometry : bond 0.00353 ( 5096) covalent geometry : angle 0.71147 ( 6906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8629 (t0) cc_final: 0.8329 (t0) REVERT: A 62 MET cc_start: 0.8476 (mtp) cc_final: 0.8264 (mmm) REVERT: A 86 LYS cc_start: 0.9416 (mmmm) cc_final: 0.9051 (mmmm) REVERT: A 87 GLU cc_start: 0.8923 (mp0) cc_final: 0.8263 (mp0) REVERT: A 110 MET cc_start: 0.8781 (ptp) cc_final: 0.7920 (ptt) REVERT: A 114 GLU cc_start: 0.8520 (tt0) cc_final: 0.8062 (tt0) REVERT: A 184 ASN cc_start: 0.8674 (m-40) cc_final: 0.8272 (t0) REVERT: A 235 ASP cc_start: 0.9174 (p0) cc_final: 0.8796 (p0) REVERT: A 236 GLU cc_start: 0.9406 (pm20) cc_final: 0.9159 (pm20) REVERT: A 248 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: A 318 ARG cc_start: 0.9497 (OUTLIER) cc_final: 0.9075 (mtp85) REVERT: B 59 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8416 (mpt) REVERT: B 70 ASP cc_start: 0.8512 (t0) cc_final: 0.8118 (p0) REVERT: B 88 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8274 (mpt-90) REVERT: B 114 GLU cc_start: 0.8120 (pt0) cc_final: 0.7646 (pt0) REVERT: B 120 LEU cc_start: 0.9329 (mt) cc_final: 0.9088 (mt) REVERT: B 136 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8395 (ptpp) REVERT: B 150 HIS cc_start: 0.7654 (t70) cc_final: 0.7319 (m90) REVERT: B 194 ASP cc_start: 0.9196 (m-30) cc_final: 0.8984 (m-30) REVERT: B 210 ARG cc_start: 0.9360 (tpp-160) cc_final: 0.9125 (tpp-160) REVERT: B 215 GLU cc_start: 0.8394 (mp0) cc_final: 0.8035 (mp0) REVERT: B 218 GLN cc_start: 0.8285 (tt0) cc_final: 0.7840 (tm-30) REVERT: B 236 GLU cc_start: 0.9510 (pm20) cc_final: 0.9232 (pm20) REVERT: B 253 ILE cc_start: 0.8998 (mm) cc_final: 0.8454 (pp) REVERT: B 259 MET cc_start: 0.7154 (mmm) cc_final: 0.6843 (mmp) REVERT: B 290 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8618 (tp30) REVERT: B 316 ILE cc_start: 0.9466 (mt) cc_final: 0.9247 (mp) outliers start: 7 outliers final: 2 residues processed: 85 average time/residue: 2.8439 time to fit residues: 249.8448 Evaluate side-chains 80 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 290 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.072565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.057838 restraints weight = 12901.092| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 4.32 r_work: 0.2914 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5104 Z= 0.150 Angle : 0.717 9.532 6912 Z= 0.361 Chirality : 0.046 0.139 758 Planarity : 0.005 0.058 918 Dihedral : 4.356 18.071 688 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.90 % Allowed : 21.51 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.34), residues: 612 helix: 0.81 (0.39), residues: 196 sheet: -2.70 (0.77), residues: 36 loop : -0.35 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 46 HIS 0.004 0.001 HIS B 119 PHE 0.009 0.001 PHE B 315 TYR 0.012 0.001 TYR A 137 ARG 0.013 0.001 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 178) hydrogen bonds : angle 5.47806 ( 462) metal coordination : bond 0.00889 ( 8) metal coordination : angle 2.12025 ( 6) covalent geometry : bond 0.00356 ( 5096) covalent geometry : angle 0.71496 ( 6906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8652 (t0) cc_final: 0.8347 (t0) REVERT: A 62 MET cc_start: 0.8426 (mtp) cc_final: 0.8224 (mmm) REVERT: A 86 LYS cc_start: 0.9432 (mmmm) cc_final: 0.9066 (mmmm) REVERT: A 110 MET cc_start: 0.8776 (ptp) cc_final: 0.7865 (ptt) REVERT: A 114 GLU cc_start: 0.8525 (tt0) cc_final: 0.7998 (tt0) REVERT: A 184 ASN cc_start: 0.8667 (m-40) cc_final: 0.8266 (t0) REVERT: A 235 ASP cc_start: 0.9160 (p0) cc_final: 0.8758 (p0) REVERT: A 236 GLU cc_start: 0.9427 (pm20) cc_final: 0.9169 (pm20) REVERT: A 248 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7666 (tp30) REVERT: A 283 ARG cc_start: 0.9083 (ttp-110) cc_final: 0.8441 (ptp-110) REVERT: A 318 ARG cc_start: 0.9500 (OUTLIER) cc_final: 0.9111 (mtp85) REVERT: B 59 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8475 (mpt) REVERT: B 70 ASP cc_start: 0.8490 (t0) cc_final: 0.7893 (p0) REVERT: B 114 GLU cc_start: 0.8202 (pt0) cc_final: 0.7120 (pm20) REVERT: B 120 LEU cc_start: 0.9328 (mt) cc_final: 0.9079 (mt) REVERT: B 136 LYS cc_start: 0.8742 (mtmm) cc_final: 0.8477 (ptpp) REVERT: B 194 ASP cc_start: 0.9220 (m-30) cc_final: 0.8988 (m-30) REVERT: B 210 ARG cc_start: 0.9379 (tpp-160) cc_final: 0.9166 (tpp-160) REVERT: B 215 GLU cc_start: 0.8350 (mp0) cc_final: 0.7978 (mp0) REVERT: B 218 GLN cc_start: 0.8294 (tt0) cc_final: 0.7929 (tm-30) REVERT: B 236 GLU cc_start: 0.9516 (pm20) cc_final: 0.9227 (pm20) REVERT: B 253 ILE cc_start: 0.9004 (mm) cc_final: 0.8442 (pp) REVERT: B 290 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8600 (tp30) REVERT: B 316 ILE cc_start: 0.9544 (mt) cc_final: 0.9318 (mp) outliers start: 5 outliers final: 3 residues processed: 83 average time/residue: 1.6495 time to fit residues: 141.3236 Evaluate side-chains 84 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 290 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.057830 restraints weight = 13238.366| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 4.38 r_work: 0.2902 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5104 Z= 0.161 Angle : 0.738 11.864 6912 Z= 0.370 Chirality : 0.046 0.140 758 Planarity : 0.005 0.057 918 Dihedral : 4.395 17.904 688 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.25 % Allowed : 20.97 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.34), residues: 612 helix: 0.77 (0.39), residues: 196 sheet: -2.86 (0.76), residues: 36 loop : -0.30 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 46 HIS 0.003 0.001 HIS B 119 PHE 0.009 0.001 PHE B 315 TYR 0.009 0.001 TYR A 288 ARG 0.013 0.001 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 178) hydrogen bonds : angle 5.49775 ( 462) metal coordination : bond 0.01207 ( 8) metal coordination : angle 2.14590 ( 6) covalent geometry : bond 0.00381 ( 5096) covalent geometry : angle 0.73533 ( 6906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5639.00 seconds wall clock time: 106 minutes 20.00 seconds (6380.00 seconds total)