Starting phenix.real_space_refine on Thu Jul 2 09:17:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nzt_49959/07_2026/9nzt_49959.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nzt_49959/07_2026/9nzt_49959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nzt_49959/07_2026/9nzt_49959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nzt_49959/07_2026/9nzt_49959.map" model { file = "/net/cci-nas-00/data/ceres_data/9nzt_49959/07_2026/9nzt_49959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nzt_49959/07_2026/9nzt_49959.cif" } resolution = 3.27 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= 0.013 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 146 5.49 5 S 33 5.16 5 C 4448 2.51 5 N 1437 2.21 5 O 1862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7927 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3386 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 11, 'TRANS': 411} Chain: "B" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1430 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain breaks: 2 Chain: "C" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "E" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2616 Classifications: {'RNA': 122} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 8, 'rna3p_pur': 58, 'rna3p_pyr': 44} Link IDs: {'rna2p': 20, 'rna3p': 101} Chain breaks: 1 Chain: "A" 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 3013 SG CYS A 377 17.508 84.302 72.414 1.00139.47 S ATOM 3036 SG CYS A 380 14.551 86.975 71.158 1.00149.32 S ATOM 3157 SG CYS A 396 18.270 87.848 71.320 1.00146.29 S ATOM 3179 SG CYS A 399 16.413 87.527 74.240 1.00145.39 S Time building chain proxies: 1.61, per 1000 atoms: 0.20 Number of scatterers: 7927 At special positions: 0 Unit cell: (84.6, 99.64, 121.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 146 15.00 O 1862 8.00 N 1437 7.00 C 4448 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: 0.57 Conformation dependent library (CDL) restraints added in 220.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 399 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 396 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 380 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 377 " Number of angles added : 6 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 7 sheets defined 48.7% alpha, 8.4% beta 42 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 25 through 62 removed outlier: 3.730A pdb=" N ARG A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.734A pdb=" N GLU A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.752A pdb=" N HIS A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN A 88 " --> pdb=" O CYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 removed outlier: 3.669A pdb=" N LYS A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 250 through 271 removed outlier: 3.767A pdb=" N ALA A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 287 through 319 Processing helix chain 'A' and resid 347 through 361 removed outlier: 3.574A pdb=" N GLU A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.585A pdb=" N ARG A 388 " --> pdb=" O LYS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.845A pdb=" N ILE A 415 " --> pdb=" O GLN A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 removed outlier: 3.907A pdb=" N ILE A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 54 Processing helix chain 'B' and resid 77 through 89 removed outlier: 4.175A pdb=" N GLY B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN B 88 " --> pdb=" O CYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 111 removed outlier: 3.545A pdb=" N LYS B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 117 Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 178 through 188 removed outlier: 3.787A pdb=" N ASN B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 3.544A pdb=" N PHE A 205 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N CYS A 195 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 198 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 131 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 141 removed outlier: 3.689A pdb=" N ILE A 148 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 226 removed outlier: 6.065A pdb=" N LEU A 225 " --> pdb=" O GLN A 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 235 through 237 removed outlier: 3.736A pdb=" N LEU A 235 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.989A pdb=" N ALA A 403 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 15 removed outlier: 3.709A pdb=" N PHE B 205 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 140 removed outlier: 3.531A pdb=" N MET B 171 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 152 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE B 169 " --> pdb=" O THR B 152 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 666 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1643 1.33 - 1.45: 2712 1.45 - 1.58: 3703 1.58 - 1.70: 288 1.70 - 1.82: 50 Bond restraints: 8396 Sorted by residual: bond pdb=" N9 A E 99 " pdb=" C4 A E 99 " ideal model delta sigma weight residual 1.374 1.398 -0.024 6.00e-03 2.78e+04 1.55e+01 bond pdb=" N9 A E 40 " pdb=" C4 A E 40 " ideal model delta sigma weight residual 1.374 1.395 -0.021 6.00e-03 2.78e+04 1.27e+01 bond pdb=" N9 A E 83 " pdb=" C4 A E 83 " ideal model delta sigma weight residual 1.374 1.395 -0.021 6.00e-03 2.78e+04 1.20e+01 bond pdb=" C3' DC C 33 " pdb=" C2' DC C 33 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.51e+00 bond pdb=" C3' DA C 36 " pdb=" C2' DA C 36 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.22e+00 ... (remaining 8391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 11828 3.54 - 7.07: 166 7.07 - 10.61: 21 10.61 - 14.15: 3 14.15 - 17.69: 1 Bond angle restraints: 12019 Sorted by residual: angle pdb=" N1 C E 66 " pdb=" C2 C E 66 " pdb=" O2 C E 66 " ideal model delta sigma weight residual 118.90 124.00 -5.10 6.00e-01 2.78e+00 7.22e+01 angle pdb=" C2 C E 13 " pdb=" N1 C E 13 " pdb=" C6 C E 13 " ideal model delta sigma weight residual 120.30 117.31 2.99 4.00e-01 6.25e+00 5.58e+01 angle pdb=" C1' C E 70 " pdb=" N1 C E 70 " pdb=" C2 C E 70 " ideal model delta sigma weight residual 118.80 126.63 -7.83 1.10e+00 8.26e-01 5.07e+01 angle pdb=" O2 C E 66 " pdb=" C2 C E 66 " pdb=" N3 C E 66 " ideal model delta sigma weight residual 121.90 117.16 4.74 7.00e-01 2.04e+00 4.58e+01 angle pdb=" C1' C E 66 " pdb=" N1 C E 66 " pdb=" C2 C E 66 " ideal model delta sigma weight residual 118.80 126.13 -7.33 1.10e+00 8.26e-01 4.44e+01 ... (remaining 12014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.50: 4483 32.50 - 65.01: 583 65.01 - 97.51: 58 97.51 - 130.02: 3 130.02 - 162.52: 5 Dihedral angle restraints: 5132 sinusoidal: 3391 harmonic: 1741 Sorted by residual: dihedral pdb=" O4' C E 19 " pdb=" C1' C E 19 " pdb=" N1 C E 19 " pdb=" C2 C E 19 " ideal model delta sinusoidal sigma weight residual 200.00 44.12 155.88 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' U E 86 " pdb=" C1' U E 86 " pdb=" N1 U E 86 " pdb=" C2 U E 86 " ideal model delta sinusoidal sigma weight residual -128.00 32.70 -160.70 1 1.70e+01 3.46e-03 6.46e+01 dihedral pdb=" CA PRO A 213 " pdb=" C PRO A 213 " pdb=" N PRO A 214 " pdb=" CA PRO A 214 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 5129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1067 0.049 - 0.099: 266 0.099 - 0.148: 58 0.148 - 0.197: 14 0.197 - 0.246: 5 Chirality restraints: 1410 Sorted by residual: chirality pdb=" C3' A E 67 " pdb=" C4' A E 67 " pdb=" O3' A E 67 " pdb=" C2' A E 67 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" P C E 68 " pdb=" OP1 C E 68 " pdb=" OP2 C E 68 " pdb=" O5' C E 68 " both_signs ideal model delta sigma weight residual True 2.41 -2.65 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C3' G E 28 " pdb=" C4' G E 28 " pdb=" O3' G E 28 " pdb=" C2' G E 28 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1407 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G E 127 " 0.023 2.00e-02 2.50e+03 2.15e-02 1.39e+01 pdb=" N9 G E 127 " -0.003 2.00e-02 2.50e+03 pdb=" C8 G E 127 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G E 127 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G E 127 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G E 127 " -0.018 2.00e-02 2.50e+03 pdb=" O6 G E 127 " 0.028 2.00e-02 2.50e+03 pdb=" N1 G E 127 " 0.014 2.00e-02 2.50e+03 pdb=" C2 G E 127 " -0.054 2.00e-02 2.50e+03 pdb=" N2 G E 127 " 0.027 2.00e-02 2.50e+03 pdb=" N3 G E 127 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G E 127 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 213 " 0.049 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO A 214 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 214 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 214 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 328 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" CG ASP A 328 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP A 328 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 328 " -0.017 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2887 2.92 - 3.41: 7409 3.41 - 3.91: 14853 3.91 - 4.40: 15906 4.40 - 4.90: 23562 Nonbonded interactions: 64617 Sorted by model distance: nonbonded pdb=" N ARG A 201 " pdb=" O ARG A 201 " model vdw 2.420 2.496 nonbonded pdb=" N1 A E 34 " pdb=" O6 G E 64 " model vdw 2.478 2.496 nonbonded pdb=" N ARG B 201 " pdb=" O ARG B 201 " model vdw 2.489 2.496 nonbonded pdb=" O4' C E 70 " pdb=" C6 C E 70 " model vdw 2.506 2.672 nonbonded pdb=" O5' G E 61 " pdb=" O4' G E 61 " model vdw 2.514 2.432 ... (remaining 64612 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.100 Find NCS groups from input model: 0.020 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8400 Z= 0.326 Angle : 1.070 17.685 12025 Z= 0.769 Chirality : 0.049 0.246 1410 Planarity : 0.008 0.088 992 Dihedral : 23.983 162.521 4012 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.96 % Allowed : 27.50 % Favored : 71.54 % 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: -0.94 (0.35), residues: 590 helix: 1.26 (0.32), residues: 261 sheet: -2.13 (0.48), residues: 111 loop : -2.11 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG B 15 TYR 0.041 0.003 TYR A 125 PHE 0.039 0.002 PHE A 182 TRP 0.029 0.004 TRP A 31 HIS 0.021 0.002 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.33 ( 8396) covalent geometry : angle 1.05200 / 0.77 (12019) hydrogen bonds : bond 0.15040 / 9.31 ( 337) hydrogen bonds : angle 5.39346 / 3.89 ( 874) metal coordination : bond 0.01882 / 0.95 ( 4) metal coordination : angle 8.73392 / 3.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 THR cc_start: 0.8311 (p) cc_final: 0.8097 (t) outliers start: 5 outliers final: 1 residues processed: 124 average time/residue: 0.0981 time to fit residues: 15.6609 Evaluate side-chains 90 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 HIS B 25 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.087518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.067035 restraints weight = 28802.797| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.12 r_work: 0.3167 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8400 Z= 0.178 Angle : 0.681 12.746 12025 Z= 0.378 Chirality : 0.039 0.197 1410 Planarity : 0.005 0.053 992 Dihedral : 24.784 164.218 2812 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.88 % Allowed : 27.88 % Favored : 69.23 % 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: -0.38 (0.35), residues: 590 helix: 1.66 (0.33), residues: 263 sheet: -1.76 (0.48), residues: 103 loop : -1.84 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 117 TYR 0.021 0.002 TYR A 199 PHE 0.018 0.003 PHE B 158 TRP 0.019 0.002 TRP A 31 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 ( 8396) covalent geometry : angle 0.66498 / 0.38 (12019) hydrogen bonds : bond 0.06192 / 4.01 ( 337) hydrogen bonds : angle 4.35432 / 3.20 ( 874) metal coordination : bond 0.01258 / 0.62 ( 4) metal coordination : angle 6.66356 / 2.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8801 (ttt180) REVERT: A 128 ASN cc_start: 0.8884 (t0) cc_final: 0.8665 (m-40) REVERT: A 135 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.9030 (ptpt) REVERT: A 211 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.6973 (tppt) REVERT: B 51 TRP cc_start: 0.9010 (t60) cc_final: 0.8329 (t-100) REVERT: B 114 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8113 (mm-30) REVERT: B 196 GLN cc_start: 0.8058 (mp10) cc_final: 0.7734 (mp10) REVERT: B 199 TYR cc_start: 0.7221 (m-10) cc_final: 0.6989 (m-80) REVERT: B 207 PHE cc_start: 0.7151 (m-80) cc_final: 0.6899 (m-80) outliers start: 15 outliers final: 5 residues processed: 107 average time/residue: 0.0918 time to fit residues: 12.6505 Evaluate side-chains 93 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 137 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 0.0010 chunk 60 optimal weight: 10.0000 chunk 14 optimal weight: 0.0060 chunk 26 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 0.0040 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 50 GLN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.088613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.068401 restraints weight = 28212.303| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.09 r_work: 0.3197 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8400 Z= 0.130 Angle : 0.632 12.501 12025 Z= 0.345 Chirality : 0.037 0.227 1410 Planarity : 0.005 0.049 992 Dihedral : 24.776 169.419 2810 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.65 % Allowed : 27.69 % Favored : 68.65 % 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: -0.16 (0.35), residues: 590 helix: 1.77 (0.33), residues: 263 sheet: -1.36 (0.47), residues: 103 loop : -1.81 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 343 TYR 0.017 0.001 TYR A 199 PHE 0.011 0.001 PHE A 338 TRP 0.030 0.002 TRP A 31 HIS 0.008 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 8396) covalent geometry : angle 0.61770 / 0.34 (12019) hydrogen bonds : bond 0.05535 / 3.64 ( 337) hydrogen bonds : angle 4.07822 / 2.99 ( 874) metal coordination : bond 0.01167 / 0.58 ( 4) metal coordination : angle 6.03725 / 2.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8776 (ttt180) REVERT: A 31 TRP cc_start: 0.8268 (m-10) cc_final: 0.7866 (m-90) REVERT: A 117 ARG cc_start: 0.8132 (tmm160) cc_final: 0.7914 (ttp80) REVERT: A 128 ASN cc_start: 0.8757 (t0) cc_final: 0.8518 (m-40) REVERT: A 135 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9031 (ptpt) REVERT: A 211 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.6772 (tppt) REVERT: A 314 ASP cc_start: 0.9030 (m-30) cc_final: 0.8731 (m-30) REVERT: B 51 TRP cc_start: 0.9034 (t60) cc_final: 0.8332 (t-100) REVERT: B 91 ASP cc_start: 0.9018 (m-30) cc_final: 0.8629 (t0) REVERT: B 114 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8011 (mm-30) REVERT: B 199 TYR cc_start: 0.7199 (m-10) cc_final: 0.6829 (m-80) REVERT: B 207 PHE cc_start: 0.7385 (m-80) cc_final: 0.6723 (m-80) outliers start: 19 outliers final: 11 residues processed: 97 average time/residue: 0.1031 time to fit residues: 13.2554 Evaluate side-chains 97 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.085709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.064859 restraints weight = 28911.950| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.11 r_work: 0.3125 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8400 Z= 0.194 Angle : 0.642 14.210 12025 Z= 0.346 Chirality : 0.038 0.189 1410 Planarity : 0.005 0.056 992 Dihedral : 24.727 168.268 2810 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.00 % Allowed : 27.12 % Favored : 67.88 % 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: -0.05 (0.35), residues: 590 helix: 1.89 (0.33), residues: 257 sheet: -1.23 (0.47), residues: 103 loop : -1.73 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 160 TYR 0.026 0.002 TYR A 199 PHE 0.022 0.002 PHE B 158 TRP 0.019 0.002 TRP A 31 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 ( 8396) covalent geometry : angle 0.62607 / 0.35 (12019) hydrogen bonds : bond 0.05287 / 3.46 ( 337) hydrogen bonds : angle 3.99265 / 2.94 ( 874) metal coordination : bond 0.01133 / 0.54 ( 4) metal coordination : angle 6.34361 / 2.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8743 (ttt180) REVERT: A 31 TRP cc_start: 0.8700 (m-10) cc_final: 0.8279 (m-10) REVERT: A 117 ARG cc_start: 0.8260 (tmm160) cc_final: 0.8050 (ttp80) REVERT: A 135 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.9016 (ptpt) REVERT: A 211 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7249 (tppt) REVERT: A 314 ASP cc_start: 0.9038 (m-30) cc_final: 0.8730 (m-30) REVERT: B 51 TRP cc_start: 0.9078 (t60) cc_final: 0.8398 (t-100) REVERT: B 114 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8135 (mm-30) REVERT: B 136 ASN cc_start: 0.9311 (t0) cc_final: 0.8878 (t0) REVERT: B 199 TYR cc_start: 0.7316 (m-10) cc_final: 0.6928 (m-80) REVERT: B 207 PHE cc_start: 0.7627 (m-80) cc_final: 0.6949 (m-80) outliers start: 26 outliers final: 13 residues processed: 98 average time/residue: 0.0704 time to fit residues: 9.2034 Evaluate side-chains 93 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 195 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 43 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.081171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.060057 restraints weight = 28784.027| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.05 r_work: 0.3028 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 8400 Z= 0.311 Angle : 0.764 15.808 12025 Z= 0.407 Chirality : 0.042 0.228 1410 Planarity : 0.006 0.054 992 Dihedral : 24.793 163.595 2810 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.96 % Allowed : 28.08 % Favored : 65.96 % 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: -0.41 (0.34), residues: 590 helix: 1.27 (0.31), residues: 261 sheet: -1.12 (0.50), residues: 101 loop : -1.69 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 179 TYR 0.042 0.003 TYR A 199 PHE 0.021 0.003 PHE B 49 TRP 0.024 0.003 TRP B 204 HIS 0.007 0.002 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.31 ( 8396) covalent geometry : angle 0.74250 / 0.41 (12019) hydrogen bonds : bond 0.06129 / 4.06 ( 337) hydrogen bonds : angle 4.26720 / 3.14 ( 874) metal coordination : bond 0.01634 / 0.75 ( 4) metal coordination : angle 8.18487 / 3.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9104 (ptpt) REVERT: A 211 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7207 (tptt) REVERT: A 371 ARG cc_start: 0.8999 (tpm170) cc_final: 0.8730 (tpm170) REVERT: B 15 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8278 (mtp85) REVERT: B 136 ASN cc_start: 0.9347 (t0) cc_final: 0.8995 (t0) outliers start: 31 outliers final: 20 residues processed: 99 average time/residue: 0.0839 time to fit residues: 11.0831 Evaluate side-chains 100 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 210 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 GLN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.083822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.062820 restraints weight = 29351.209| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.09 r_work: 0.3093 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8400 Z= 0.145 Angle : 0.644 14.017 12025 Z= 0.346 Chirality : 0.038 0.205 1410 Planarity : 0.005 0.052 992 Dihedral : 24.699 171.200 2810 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.85 % Allowed : 29.81 % Favored : 66.35 % 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: 0.16 (0.35), residues: 590 helix: 1.97 (0.32), residues: 255 sheet: -0.94 (0.50), residues: 98 loop : -1.55 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 201 TYR 0.029 0.002 TYR A 199 PHE 0.012 0.001 PHE B 207 TRP 0.014 0.001 TRP A 31 HIS 0.002 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 8396) covalent geometry : angle 0.62978 / 0.34 (12019) hydrogen bonds : bond 0.05332 / 3.51 ( 337) hydrogen bonds : angle 3.87315 / 2.87 ( 874) metal coordination : bond 0.01041 / 0.50 ( 4) metal coordination : angle 6.01791 / 2.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9106 (ptpt) REVERT: A 211 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7378 (tppt) REVERT: A 371 ARG cc_start: 0.9031 (tpm170) cc_final: 0.8757 (tpm170) REVERT: B 16 TYR cc_start: 0.6952 (p90) cc_final: 0.6152 (p90) REVERT: B 51 TRP cc_start: 0.9072 (t60) cc_final: 0.8526 (t-100) REVERT: B 82 TYR cc_start: 0.9190 (t80) cc_final: 0.8954 (t80) REVERT: B 136 ASN cc_start: 0.9400 (t0) cc_final: 0.9055 (t0) REVERT: B 199 TYR cc_start: 0.7438 (m-80) cc_final: 0.7175 (m-80) outliers start: 20 outliers final: 13 residues processed: 88 average time/residue: 0.0838 time to fit residues: 9.8353 Evaluate side-chains 85 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 212 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 14 optimal weight: 0.0670 chunk 23 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.085056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064272 restraints weight = 28595.340| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.09 r_work: 0.3132 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8400 Z= 0.121 Angle : 0.616 16.347 12025 Z= 0.331 Chirality : 0.037 0.225 1410 Planarity : 0.004 0.043 992 Dihedral : 24.636 174.045 2810 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.00 % Allowed : 29.42 % Favored : 65.58 % 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: 0.13 (0.35), residues: 590 helix: 2.04 (0.33), residues: 255 sheet: -0.97 (0.46), residues: 108 loop : -1.70 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 179 TYR 0.021 0.002 TYR A 199 PHE 0.012 0.001 PHE A 338 TRP 0.010 0.001 TRP A 31 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 ( 8396) covalent geometry : angle 0.60534 / 0.33 (12019) hydrogen bonds : bond 0.04989 / 3.31 ( 337) hydrogen bonds : angle 3.70187 / 2.74 ( 874) metal coordination : bond 0.00931 / 0.47 ( 4) metal coordination : angle 5.17202 / 2.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9122 (ptpt) REVERT: A 211 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7274 (tppt) REVERT: A 314 ASP cc_start: 0.8983 (m-30) cc_final: 0.8671 (m-30) REVERT: A 371 ARG cc_start: 0.9060 (tpm170) cc_final: 0.8778 (tpm170) REVERT: B 15 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8242 (mtp-110) REVERT: B 16 TYR cc_start: 0.6938 (p90) cc_final: 0.6255 (p90) REVERT: B 51 TRP cc_start: 0.9061 (t60) cc_final: 0.8321 (t-100) REVERT: B 120 MET cc_start: 0.8778 (tmm) cc_final: 0.8370 (tmm) REVERT: B 134 ASP cc_start: 0.7359 (t0) cc_final: 0.7145 (t0) REVERT: B 154 PHE cc_start: 0.8550 (m-10) cc_final: 0.8153 (p90) REVERT: B 199 TYR cc_start: 0.7319 (m-80) cc_final: 0.7034 (m-80) outliers start: 26 outliers final: 16 residues processed: 86 average time/residue: 0.0844 time to fit residues: 9.7376 Evaluate side-chains 88 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 212 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 53 optimal weight: 9.9990 chunk 21 optimal weight: 0.4980 chunk 46 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 GLN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** 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 = 0.3757 r_free = 0.3757 target = 0.083496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.062623 restraints weight = 28605.192| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.07 r_work: 0.3089 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8400 Z= 0.180 Angle : 0.639 13.889 12025 Z= 0.342 Chirality : 0.037 0.197 1410 Planarity : 0.005 0.063 992 Dihedral : 24.611 171.439 2810 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.62 % Allowed : 30.19 % Favored : 65.19 % 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: 0.23 (0.36), residues: 590 helix: 2.06 (0.32), residues: 255 sheet: -0.77 (0.48), residues: 108 loop : -1.64 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 201 TYR 0.023 0.002 TYR A 199 PHE 0.011 0.001 PHE B 49 TRP 0.011 0.001 TRP B 204 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 ( 8396) covalent geometry : angle 0.62650 / 0.34 (12019) hydrogen bonds : bond 0.05081 / 3.35 ( 337) hydrogen bonds : angle 3.78471 / 2.80 ( 874) metal coordination : bond 0.01010 / 0.49 ( 4) metal coordination : angle 5.76363 / 2.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.9091 (ptpt) REVERT: A 211 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7390 (tppt) REVERT: A 371 ARG cc_start: 0.9011 (tpm170) cc_final: 0.8736 (tpm170) REVERT: B 15 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8588 (mtp-110) REVERT: B 51 TRP cc_start: 0.9060 (t60) cc_final: 0.8481 (t-100) REVERT: B 207 PHE cc_start: 0.7909 (m-80) cc_final: 0.7165 (m-80) outliers start: 24 outliers final: 17 residues processed: 84 average time/residue: 0.0871 time to fit residues: 9.7750 Evaluate side-chains 89 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 210 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 65 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 GLN A 184 ASN ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.084787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.063891 restraints weight = 29165.674| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.08 r_work: 0.3119 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8400 Z= 0.129 Angle : 0.608 13.959 12025 Z= 0.328 Chirality : 0.036 0.197 1410 Planarity : 0.004 0.043 992 Dihedral : 24.599 174.525 2810 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.65 % Allowed : 30.38 % Favored : 65.96 % 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: 0.28 (0.35), residues: 590 helix: 2.12 (0.33), residues: 255 sheet: -0.69 (0.48), residues: 108 loop : -1.68 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 117 TYR 0.018 0.001 TYR A 199 PHE 0.010 0.001 PHE A 338 TRP 0.007 0.001 TRP A 51 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 8396) covalent geometry : angle 0.59726 / 0.33 (12019) hydrogen bonds : bond 0.04963 / 3.29 ( 337) hydrogen bonds : angle 3.65938 / 2.71 ( 874) metal coordination : bond 0.00895 / 0.45 ( 4) metal coordination : angle 5.13006 / 2.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9106 (ptpt) REVERT: A 211 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7339 (tppt) REVERT: A 314 ASP cc_start: 0.8957 (m-30) cc_final: 0.8649 (m-30) REVERT: A 371 ARG cc_start: 0.9050 (tpm170) cc_final: 0.8780 (tpm170) REVERT: B 51 TRP cc_start: 0.9002 (t60) cc_final: 0.8442 (t-100) REVERT: B 207 PHE cc_start: 0.7880 (m-80) cc_final: 0.7119 (m-80) outliers start: 19 outliers final: 13 residues processed: 84 average time/residue: 0.0981 time to fit residues: 11.0383 Evaluate side-chains 82 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 210 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 0.0070 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN ** A 217 HIS ** 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 = 0.3792 r_free = 0.3792 target = 0.085294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.064598 restraints weight = 28604.066| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.09 r_work: 0.3142 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8400 Z= 0.124 Angle : 0.636 16.176 12025 Z= 0.336 Chirality : 0.036 0.195 1410 Planarity : 0.005 0.085 992 Dihedral : 24.582 175.480 2810 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.08 % Allowed : 31.15 % Favored : 65.77 % 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: 0.29 (0.35), residues: 590 helix: 2.09 (0.33), residues: 255 sheet: -0.61 (0.48), residues: 108 loop : -1.67 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 201 TYR 0.025 0.001 TYR A 199 PHE 0.017 0.001 PHE B 158 TRP 0.007 0.001 TRP A 51 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 8396) covalent geometry : angle 0.62675 / 0.34 (12019) hydrogen bonds : bond 0.04900 / 3.26 ( 337) hydrogen bonds : angle 3.65863 / 2.71 ( 874) metal coordination : bond 0.00897 / 0.45 ( 4) metal coordination : angle 4.94799 / 2.18 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9131 (ptpt) REVERT: A 211 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7256 (tppt) REVERT: A 314 ASP cc_start: 0.8967 (m-30) cc_final: 0.8657 (m-30) REVERT: A 371 ARG cc_start: 0.9042 (tpm170) cc_final: 0.8762 (tpm170) REVERT: B 15 ARG cc_start: 0.9003 (mtp-110) cc_final: 0.8536 (mtp-110) REVERT: B 51 TRP cc_start: 0.9012 (t60) cc_final: 0.8442 (t-100) outliers start: 16 outliers final: 14 residues processed: 83 average time/residue: 0.1148 time to fit residues: 12.3305 Evaluate side-chains 84 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 210 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 184 ASN ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.084445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.063706 restraints weight = 28557.374| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.06 r_work: 0.3121 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8400 Z= 0.157 Angle : 0.645 15.935 12025 Z= 0.344 Chirality : 0.037 0.221 1410 Planarity : 0.005 0.045 992 Dihedral : 24.573 173.927 2810 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.08 % Allowed : 30.77 % Favored : 66.15 % 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: 0.25 (0.35), residues: 590 helix: 1.95 (0.32), residues: 262 sheet: -0.51 (0.49), residues: 108 loop : -1.73 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.031 0.002 TYR A 199 PHE 0.026 0.001 PHE B 207 TRP 0.007 0.001 TRP A 51 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 ( 8396) covalent geometry : angle 0.63448 / 0.34 (12019) hydrogen bonds : bond 0.04951 / 3.27 ( 337) hydrogen bonds : angle 3.78805 / 2.80 ( 874) metal coordination : bond 0.00914 / 0.45 ( 4) metal coordination : angle 5.25806 / 2.30 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1755.18 seconds wall clock time: 30 minutes 51.04 seconds (1851.04 seconds total)