Starting phenix.real_space_refine on Wed Mar 4 09:27:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s2e_10088/03_2026/6s2e_10088.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s2e_10088/03_2026/6s2e_10088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6s2e_10088/03_2026/6s2e_10088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s2e_10088/03_2026/6s2e_10088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s2e_10088/03_2026/6s2e_10088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s2e_10088/03_2026/6s2e_10088.map" } resolution = 4.2 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= 0.008 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 Fe 4 7.16 5 S 68 5.16 5 C 7984 2.51 5 N 2079 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12459 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 8154 Classifications: {'peptide': 1006} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 957} Chain breaks: 6 Chain: "D" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 225 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "B" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3041 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4761 SG CYS A 677 74.994 35.130 17.630 1.00143.72 S ATOM 4690 SG CYS A 668 72.088 29.439 18.791 1.00135.31 S ATOM 4963 SG CYS A 763 75.014 33.159 23.280 1.00114.07 S ATOM 4673 SG CYS A 665 77.473 29.916 18.710 1.00136.78 S Time building chain proxies: 3.02, per 1000 atoms: 0.24 Number of scatterers: 12459 At special positions: 0 Unit cell: (126.557, 128.684, 103.16, 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) Fe 4 26.01 S 68 16.00 O 2324 8.00 N 2079 7.00 C 7984 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: 0.98 Conformation dependent library (CDL) restraints added in 471.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1401 " pdb="FE1 SF4 A1401 " - pdb=" SG CYS A 677 " pdb="FE4 SF4 A1401 " - pdb=" SG CYS A 665 " pdb="FE3 SF4 A1401 " - pdb=" SG CYS A 763 " pdb="FE2 SF4 A1401 " - pdb=" SG CYS A 668 " Number of angles added : 12 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 0 sheets defined 42.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 195 through 212 Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 354 through 370 Processing helix chain 'A' and resid 382 through 394 removed outlier: 3.542A pdb=" N PHE A 386 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 455 through 466 Proline residue: A 461 - end of helix removed outlier: 4.051A pdb=" N PHE A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 498 removed outlier: 3.618A pdb=" N LEU A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N HIS A 490 " --> pdb=" O MET A 486 " (cutoff:3.500A) Proline residue: A 491 - end of helix Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 511 through 527 Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.576A pdb=" N ILE A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 603 through 607 Processing helix chain 'A' and resid 609 through 627 Processing helix chain 'A' and resid 643 through 652 Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 769 through 798 removed outlier: 3.974A pdb=" N ILE A 798 " --> pdb=" O ASN A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 834 removed outlier: 3.710A pdb=" N PHE A 830 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR A 831 " --> pdb=" O LEU A 827 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 834 " --> pdb=" O PHE A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 869 Processing helix chain 'A' and resid 905 through 919 removed outlier: 3.868A pdb=" N THR A 919 " --> pdb=" O HIS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1006 removed outlier: 4.731A pdb=" N LYS A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A1005 " --> pdb=" O ASP A1001 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A1006 " --> pdb=" O ILE A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1032 Processing helix chain 'A' and resid 1038 through 1045 removed outlier: 3.608A pdb=" N LEU A1042 " --> pdb=" O GLU A1038 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A1043 " --> pdb=" O ASP A1039 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A1044 " --> pdb=" O GLU A1040 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A1045 " --> pdb=" O ASP A1041 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1038 through 1045' Processing helix chain 'A' and resid 1065 through 1078 removed outlier: 3.575A pdb=" N THR A1069 " --> pdb=" O THR A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1083 Processing helix chain 'A' and resid 1101 through 1105 Processing helix chain 'A' and resid 1137 through 1141 Processing helix chain 'A' and resid 1142 through 1158 Processing helix chain 'A' and resid 1158 through 1165 Processing helix chain 'A' and resid 1177 through 1184 removed outlier: 3.812A pdb=" N LYS A1181 " --> pdb=" O PRO A1177 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 45 through 51 removed outlier: 3.758A pdb=" N ARG D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 740 removed outlier: 3.647A pdb=" N LEU E 739 " --> pdb=" O THR E 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.945A pdb=" N LYS B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 181 through 199 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.597A pdb=" N THR B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 253 through 269 Processing helix chain 'B' and resid 277 through 288 removed outlier: 3.987A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 340 through 349 Proline residue: B 346 - end of helix Processing helix chain 'B' and resid 357 through 363 401 hydrogen bonds defined for protein. 1146 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: 1.59 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 5172 1.40 - 1.59: 7448 1.59 - 1.78: 8 1.78 - 1.96: 99 1.96 - 2.15: 12 Bond restraints: 12739 Sorted by residual: bond pdb=" S2 SF4 A1401 " pdb="FE4 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.098 0.182 3.00e-02 1.11e+03 3.68e+01 bond pdb=" S4 SF4 A1401 " pdb="FE1 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.100 0.180 3.00e-02 1.11e+03 3.59e+01 bond pdb=" S2 SF4 A1401 " pdb="FE3 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.117 0.163 3.00e-02 1.11e+03 2.95e+01 bond pdb=" S3 SF4 A1401 " pdb="FE2 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.67e+01 bond pdb=" S4 SF4 A1401 " pdb="FE3 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.126 0.154 3.00e-02 1.11e+03 2.62e+01 ... (remaining 12734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 16925 4.68 - 9.36: 266 9.36 - 14.04: 20 14.04 - 18.72: 6 18.72 - 23.40: 3 Bond angle restraints: 17220 Sorted by residual: angle pdb=" CA GLU A 623 " pdb=" CB GLU A 623 " pdb=" CG GLU A 623 " ideal model delta sigma weight residual 114.10 128.77 -14.67 2.00e+00 2.50e-01 5.38e+01 angle pdb=" CA LEU A1045 " pdb=" CB LEU A1045 " pdb=" CG LEU A1045 " ideal model delta sigma weight residual 116.30 139.70 -23.40 3.50e+00 8.16e-02 4.47e+01 angle pdb=" C GLU A 244 " pdb=" N TYR A 245 " pdb=" CA TYR A 245 " ideal model delta sigma weight residual 122.26 111.53 10.73 1.73e+00 3.34e-01 3.85e+01 angle pdb=" CA LEU B 87 " pdb=" CB LEU B 87 " pdb=" CG LEU B 87 " ideal model delta sigma weight residual 116.30 136.03 -19.73 3.50e+00 8.16e-02 3.18e+01 angle pdb=" C THR B 375 " pdb=" N VAL B 376 " pdb=" CA VAL B 376 " ideal model delta sigma weight residual 122.48 116.28 6.20 1.13e+00 7.83e-01 3.01e+01 ... (remaining 17215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6970 17.81 - 35.61: 603 35.61 - 53.42: 115 53.42 - 71.23: 27 71.23 - 89.03: 8 Dihedral angle restraints: 7723 sinusoidal: 3214 harmonic: 4509 Sorted by residual: dihedral pdb=" CA SER B 379 " pdb=" C SER B 379 " pdb=" N ARG B 380 " pdb=" CA ARG B 380 " ideal model delta harmonic sigma weight residual -180.00 -135.01 -44.99 0 5.00e+00 4.00e-02 8.10e+01 dihedral pdb=" CA ARG A 663 " pdb=" C ARG A 663 " pdb=" N ASP A 664 " pdb=" CA ASP A 664 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ARG A 672 " pdb=" C ARG A 672 " pdb=" N PRO A 673 " pdb=" CA PRO A 673 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 7720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.479: 1892 0.479 - 0.957: 0 0.957 - 1.436: 0 1.436 - 1.914: 0 1.914 - 2.393: 4 Chirality restraints: 1896 Sorted by residual: chirality pdb="FE4 SF4 A1401 " pdb=" S1 SF4 A1401 " pdb=" S2 SF4 A1401 " pdb=" S3 SF4 A1401 " both_signs ideal model delta sigma weight residual False 10.55 8.16 2.39 2.00e-01 2.50e+01 1.43e+02 chirality pdb="FE2 SF4 A1401 " pdb=" S1 SF4 A1401 " pdb=" S3 SF4 A1401 " pdb=" S4 SF4 A1401 " both_signs ideal model delta sigma weight residual False 10.55 8.28 2.28 2.00e-01 2.50e+01 1.30e+02 chirality pdb="FE1 SF4 A1401 " pdb=" S2 SF4 A1401 " pdb=" S3 SF4 A1401 " pdb=" S4 SF4 A1401 " both_signs ideal model delta sigma weight residual False -10.55 -8.39 -2.17 2.00e-01 2.50e+01 1.17e+02 ... (remaining 1893 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 80 " -0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C THR A 80 " 0.074 2.00e-02 2.50e+03 pdb=" O THR A 80 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN A 81 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 863 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C ALA A 863 " -0.074 2.00e-02 2.50e+03 pdb=" O ALA A 863 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A 864 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 762 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C VAL A 762 " 0.072 2.00e-02 2.50e+03 pdb=" O VAL A 762 " -0.028 2.00e-02 2.50e+03 pdb=" N CYS A 763 " -0.024 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1541 2.75 - 3.29: 12329 3.29 - 3.83: 21221 3.83 - 4.36: 24416 4.36 - 4.90: 40289 Nonbonded interactions: 99796 Sorted by model distance: nonbonded pdb=" OH TYR B 261 " pdb=" O TRP B 284 " model vdw 2.218 3.040 nonbonded pdb=" O LYS B 357 " pdb=" OG SER B 360 " model vdw 2.255 3.040 nonbonded pdb=" O TYR A 135 " pdb=" OH TYR A 249 " model vdw 2.263 3.040 nonbonded pdb=" O LEU D 73 " pdb=" OG SER B 2 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR A1068 " pdb=" O THR A1103 " model vdw 2.296 3.040 ... (remaining 99791 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=0.62 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.420 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 0.009 0.182 12743 Z= 0.405 Angle : 1.557 24.254 17232 Z= 0.848 Chirality : 0.129 2.393 1896 Planarity : 0.009 0.088 2200 Dihedral : 14.137 89.031 4799 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.19 % Rotamer: Outliers : 1.88 % Allowed : 8.38 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.45 (0.19), residues: 1517 helix: -0.89 (0.19), residues: 555 sheet: -0.40 (0.30), residues: 248 loop : -1.11 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG A 260 TYR 0.039 0.005 TYR A 245 PHE 0.058 0.004 PHE B 288 TRP 0.029 0.004 TRP A 78 HIS 0.011 0.003 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00930 (12739) covalent geometry : angle 1.52510 (17220) hydrogen bonds : bond 0.16101 ( 401) hydrogen bonds : angle 6.40056 ( 1146) metal coordination : bond 0.03913 ( 4) metal coordination : angle 11.95497 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.507 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: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8371 (m-80) cc_final: 0.7938 (m-10) REVERT: A 121 PHE cc_start: 0.8617 (m-80) cc_final: 0.8094 (m-80) REVERT: A 135 TYR cc_start: 0.8095 (t80) cc_final: 0.7468 (t80) REVERT: A 148 ARG cc_start: 0.8114 (mtp180) cc_final: 0.7894 (ptm160) REVERT: A 151 ASP cc_start: 0.7662 (m-30) cc_final: 0.7442 (m-30) REVERT: A 186 LYS cc_start: 0.8642 (tttp) cc_final: 0.8232 (tptt) REVERT: A 314 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8353 (tpp) REVERT: A 383 ASP cc_start: 0.7583 (m-30) cc_final: 0.6704 (m-30) REVERT: A 453 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8337 (tp30) REVERT: A 459 MET cc_start: 0.7464 (mtt) cc_final: 0.6782 (mtt) REVERT: A 811 LYS cc_start: 0.8802 (mttp) cc_final: 0.8497 (mttt) REVERT: A 827 LEU cc_start: 0.9539 (tt) cc_final: 0.9318 (tt) REVERT: A 955 LEU cc_start: 0.8945 (mp) cc_final: 0.8693 (mp) REVERT: A 1146 TYR cc_start: 0.8871 (m-80) cc_final: 0.8488 (m-10) REVERT: D 78 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6722 (tm-30) REVERT: D 81 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7671 (t) REVERT: D 109 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8091 (mmmt) REVERT: D 117 ASP cc_start: 0.8615 (t0) cc_final: 0.8332 (t0) REVERT: B 16 LYS cc_start: 0.8870 (mttm) cc_final: 0.8595 (mmpt) REVERT: B 232 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8652 (pt0) REVERT: B 236 ASN cc_start: 0.8921 (m-40) cc_final: 0.8382 (p0) REVERT: B 295 ASP cc_start: 0.7767 (p0) cc_final: 0.7547 (p0) outliers start: 26 outliers final: 9 residues processed: 257 average time/residue: 0.1191 time to fit residues: 43.7582 Evaluate side-chains 175 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 83 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 638 HIS A 671 ASN A 973 ASN A 999 GLN ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.085231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.069001 restraints weight = 64111.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.070628 restraints weight = 41789.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.071675 restraints weight = 31046.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.072334 restraints weight = 25438.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.072739 restraints weight = 22250.028| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12743 Z= 0.148 Angle : 0.795 34.096 17232 Z= 0.356 Chirality : 0.045 0.192 1896 Planarity : 0.005 0.052 2200 Dihedral : 5.585 70.240 1661 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.14 % Allowed : 2.60 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -0.17 (0.21), residues: 1517 helix: 0.67 (0.21), residues: 561 sheet: -0.16 (0.32), residues: 243 loop : -0.65 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 89 TYR 0.031 0.002 TYR A 412 PHE 0.018 0.002 PHE B 288 TRP 0.018 0.002 TRP A 841 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00324 (12739) covalent geometry : angle 0.68447 (17220) hydrogen bonds : bond 0.05248 ( 401) hydrogen bonds : angle 5.43415 ( 1146) metal coordination : bond 0.00234 ( 4) metal coordination : angle 15.34886 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.443 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 PHE cc_start: 0.8695 (m-80) cc_final: 0.8188 (m-80) REVERT: A 135 TYR cc_start: 0.8087 (t80) cc_final: 0.7424 (t80) REVERT: A 186 LYS cc_start: 0.8503 (tttp) cc_final: 0.8156 (tptt) REVERT: A 452 ILE cc_start: 0.7871 (tp) cc_final: 0.7175 (pt) REVERT: A 459 MET cc_start: 0.7759 (mtt) cc_final: 0.7054 (mtt) REVERT: A 505 ASP cc_start: 0.8485 (m-30) cc_final: 0.8166 (m-30) REVERT: A 517 GLU cc_start: 0.8700 (tt0) cc_final: 0.8458 (tm-30) REVERT: A 521 MET cc_start: 0.9148 (mtt) cc_final: 0.8006 (tpp) REVERT: A 811 LYS cc_start: 0.8627 (mttp) cc_final: 0.8374 (mttt) REVERT: A 909 MET cc_start: 0.8776 (ppp) cc_final: 0.8436 (ppp) REVERT: A 1023 CYS cc_start: 0.7906 (t) cc_final: 0.7664 (t) REVERT: A 1036 MET cc_start: 0.4637 (mmp) cc_final: 0.4364 (tpt) REVERT: A 1146 TYR cc_start: 0.8725 (m-80) cc_final: 0.8373 (m-10) REVERT: A 1165 GLN cc_start: 0.8109 (mp10) cc_final: 0.7555 (tm-30) REVERT: D 30 MET cc_start: 0.7722 (mmm) cc_final: 0.7210 (mmm) REVERT: D 109 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8043 (mmmt) REVERT: D 117 ASP cc_start: 0.8375 (t0) cc_final: 0.7967 (t0) REVERT: D 119 MET cc_start: 0.8763 (mmp) cc_final: 0.8344 (mmp) REVERT: B 16 LYS cc_start: 0.8940 (mttm) cc_final: 0.8684 (mmpt) REVERT: B 232 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8739 (mt-10) outliers start: 2 outliers final: 1 residues processed: 200 average time/residue: 0.1059 time to fit residues: 30.9330 Evaluate side-chains 152 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 HIS A 444 GLN A 450 ASN A1033 HIS ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.082215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.065974 restraints weight = 65359.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.067553 restraints weight = 42625.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.068583 restraints weight = 31659.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.069273 restraints weight = 25963.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.069688 restraints weight = 22664.992| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 12743 Z= 0.190 Angle : 0.787 33.148 17232 Z= 0.345 Chirality : 0.045 0.168 1896 Planarity : 0.005 0.045 2200 Dihedral : 5.307 62.173 1661 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -0.24 (0.21), residues: 1517 helix: 0.63 (0.21), residues: 564 sheet: -0.36 (0.32), residues: 258 loop : -0.65 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1147 TYR 0.026 0.002 TYR A 412 PHE 0.016 0.002 PHE A1003 TRP 0.016 0.002 TRP B 284 HIS 0.005 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00409 (12739) covalent geometry : angle 0.65972 (17220) hydrogen bonds : bond 0.04667 ( 401) hydrogen bonds : angle 5.27500 ( 1146) metal coordination : bond 0.01136 ( 4) metal coordination : angle 16.25027 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.518 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: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8864 (m-30) cc_final: 0.8491 (m-30) REVERT: A 121 PHE cc_start: 0.8784 (m-80) cc_final: 0.8378 (m-80) REVERT: A 135 TYR cc_start: 0.8157 (t80) cc_final: 0.7389 (t80) REVERT: A 186 LYS cc_start: 0.8697 (tttp) cc_final: 0.8345 (tptt) REVERT: A 415 SER cc_start: 0.8687 (p) cc_final: 0.8052 (p) REVERT: A 459 MET cc_start: 0.7813 (mtt) cc_final: 0.7276 (mtt) REVERT: A 505 ASP cc_start: 0.8379 (m-30) cc_final: 0.8126 (m-30) REVERT: A 517 GLU cc_start: 0.8869 (tt0) cc_final: 0.8357 (tm-30) REVERT: A 521 MET cc_start: 0.9262 (mtt) cc_final: 0.7803 (mtt) REVERT: A 811 LYS cc_start: 0.8678 (mttp) cc_final: 0.8358 (mttt) REVERT: A 1036 MET cc_start: 0.4943 (mmp) cc_final: 0.4693 (tpt) REVERT: A 1146 TYR cc_start: 0.8710 (m-80) cc_final: 0.8110 (m-10) REVERT: A 1165 GLN cc_start: 0.8071 (mp10) cc_final: 0.7566 (tm-30) REVERT: D 30 MET cc_start: 0.7794 (mmm) cc_final: 0.7261 (mmm) REVERT: D 81 THR cc_start: 0.8234 (t) cc_final: 0.7988 (t) REVERT: D 117 ASP cc_start: 0.8206 (t0) cc_final: 0.7911 (t0) REVERT: D 119 MET cc_start: 0.8623 (mmp) cc_final: 0.8072 (mmm) REVERT: B 16 LYS cc_start: 0.8927 (mttm) cc_final: 0.8681 (mmpt) REVERT: B 232 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8671 (mt-10) REVERT: B 356 MET cc_start: 0.7858 (mtp) cc_final: 0.7396 (ttp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.0985 time to fit residues: 27.5346 Evaluate side-chains 142 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 27 optimal weight: 0.0870 overall best weight: 3.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.080623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.064675 restraints weight = 66395.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066150 restraints weight = 44242.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.067114 restraints weight = 33440.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.067747 restraints weight = 27662.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.068095 restraints weight = 24407.201| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12743 Z= 0.224 Angle : 0.857 33.143 17232 Z= 0.359 Chirality : 0.045 0.173 1896 Planarity : 0.005 0.047 2200 Dihedral : 5.349 58.411 1661 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -0.44 (0.21), residues: 1517 helix: 0.52 (0.21), residues: 567 sheet: -0.46 (0.32), residues: 252 loop : -0.82 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 862 TYR 0.026 0.002 TYR A 412 PHE 0.020 0.002 PHE B 288 TRP 0.020 0.002 TRP B 284 HIS 0.005 0.001 HIS A1033 Details of bonding type rmsd covalent geometry : bond 0.00480 (12739) covalent geometry : angle 0.69032 (17220) hydrogen bonds : bond 0.04612 ( 401) hydrogen bonds : angle 5.26624 ( 1146) metal coordination : bond 0.01355 ( 4) metal coordination : angle 19.28446 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.491 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: A 47 ASP cc_start: 0.8718 (m-30) cc_final: 0.8433 (m-30) REVERT: A 135 TYR cc_start: 0.8116 (t80) cc_final: 0.7334 (t80) REVERT: A 186 LYS cc_start: 0.8836 (tttp) cc_final: 0.8433 (tptt) REVERT: A 415 SER cc_start: 0.8634 (p) cc_final: 0.8075 (p) REVERT: A 459 MET cc_start: 0.7687 (mtt) cc_final: 0.7157 (mtt) REVERT: A 505 ASP cc_start: 0.8335 (m-30) cc_final: 0.8090 (m-30) REVERT: A 517 GLU cc_start: 0.8916 (tt0) cc_final: 0.8407 (tm-30) REVERT: A 521 MET cc_start: 0.9376 (mtt) cc_final: 0.8624 (mtp) REVERT: A 830 PHE cc_start: 0.8931 (m-80) cc_final: 0.8717 (m-10) REVERT: A 1036 MET cc_start: 0.4827 (mmp) cc_final: 0.4563 (tpt) REVERT: A 1165 GLN cc_start: 0.8059 (mp10) cc_final: 0.7536 (tm-30) REVERT: D 30 MET cc_start: 0.7633 (mmm) cc_final: 0.6938 (mmm) REVERT: D 90 LEU cc_start: 0.9014 (mt) cc_final: 0.8790 (mt) REVERT: D 117 ASP cc_start: 0.8190 (t0) cc_final: 0.7891 (t0) REVERT: D 119 MET cc_start: 0.8537 (mmp) cc_final: 0.7733 (mmm) REVERT: B 16 LYS cc_start: 0.9022 (mttm) cc_final: 0.8699 (mmpt) REVERT: B 232 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8605 (mt-10) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.1025 time to fit residues: 27.3388 Evaluate side-chains 139 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 129 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 0.0970 chunk 148 optimal weight: 6.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** 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 = 0.3702 r_free = 0.3702 target = 0.081102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.065116 restraints weight = 66576.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.066659 restraints weight = 43816.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.067665 restraints weight = 32823.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.068301 restraints weight = 27048.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.068634 restraints weight = 23796.685| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12743 Z= 0.169 Angle : 0.786 31.129 17232 Z= 0.329 Chirality : 0.045 0.211 1896 Planarity : 0.005 0.050 2200 Dihedral : 5.211 55.183 1661 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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 (0.21), residues: 1517 helix: 0.63 (0.21), residues: 568 sheet: -0.50 (0.33), residues: 250 loop : -0.82 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 806 TYR 0.020 0.002 TYR A1146 PHE 0.026 0.002 PHE A 594 TRP 0.015 0.002 TRP B 284 HIS 0.004 0.001 HIS A1033 Details of bonding type rmsd covalent geometry : bond 0.00364 (12739) covalent geometry : angle 0.63265 (17220) hydrogen bonds : bond 0.04295 ( 401) hydrogen bonds : angle 5.12977 ( 1146) metal coordination : bond 0.01080 ( 4) metal coordination : angle 17.71546 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.496 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: A 47 ASP cc_start: 0.8609 (m-30) cc_final: 0.8259 (m-30) REVERT: A 135 TYR cc_start: 0.8034 (t80) cc_final: 0.7330 (t80) REVERT: A 186 LYS cc_start: 0.8901 (tttp) cc_final: 0.8277 (tptt) REVERT: A 193 PHE cc_start: 0.7425 (m-10) cc_final: 0.6897 (m-10) REVERT: A 415 SER cc_start: 0.8513 (p) cc_final: 0.7875 (p) REVERT: A 459 MET cc_start: 0.7536 (mtt) cc_final: 0.6964 (mtt) REVERT: A 483 TYR cc_start: 0.8494 (m-80) cc_final: 0.8216 (m-10) REVERT: A 505 ASP cc_start: 0.8283 (m-30) cc_final: 0.8075 (m-30) REVERT: A 517 GLU cc_start: 0.8875 (tt0) cc_final: 0.8460 (tm-30) REVERT: A 1165 GLN cc_start: 0.8055 (mp10) cc_final: 0.7537 (tm-30) REVERT: D 117 ASP cc_start: 0.8085 (t0) cc_final: 0.7859 (t0) REVERT: D 119 MET cc_start: 0.8550 (mmp) cc_final: 0.7770 (mmm) REVERT: E 724 GLU cc_start: 0.8275 (pm20) cc_final: 0.7944 (pm20) REVERT: B 16 LYS cc_start: 0.8978 (mttm) cc_final: 0.8688 (mmpt) REVERT: B 52 CYS cc_start: 0.8044 (p) cc_final: 0.7732 (t) REVERT: B 232 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8561 (mt-10) REVERT: B 323 MET cc_start: 0.8117 (mmm) cc_final: 0.7853 (mmm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1091 time to fit residues: 28.1992 Evaluate side-chains 140 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 119 optimal weight: 0.0870 chunk 90 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 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 = 0.3670 r_free = 0.3670 target = 0.079589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.063939 restraints weight = 67501.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065412 restraints weight = 44715.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.066387 restraints weight = 33641.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066956 restraints weight = 27788.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.067394 restraints weight = 24571.492| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12743 Z= 0.223 Angle : 0.841 31.815 17232 Z= 0.354 Chirality : 0.045 0.172 1896 Planarity : 0.005 0.050 2200 Dihedral : 5.326 49.117 1661 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.07 % Allowed : 2.24 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -0.56 (0.21), residues: 1517 helix: 0.45 (0.21), residues: 567 sheet: -0.54 (0.33), residues: 243 loop : -0.92 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 679 TYR 0.027 0.002 TYR A 770 PHE 0.025 0.002 PHE A 777 TRP 0.024 0.002 TRP B 284 HIS 0.005 0.001 HIS A1033 Details of bonding type rmsd covalent geometry : bond 0.00476 (12739) covalent geometry : angle 0.68031 (17220) hydrogen bonds : bond 0.04474 ( 401) hydrogen bonds : angle 5.26355 ( 1146) metal coordination : bond 0.01354 ( 4) metal coordination : angle 18.77245 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.452 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: symmetry clash REVERT: A 47 ASP cc_start: 0.8654 (m-30) cc_final: 0.8343 (m-30) REVERT: A 135 TYR cc_start: 0.8090 (t80) cc_final: 0.7410 (t80) REVERT: A 186 LYS cc_start: 0.8979 (tttp) cc_final: 0.8299 (tptt) REVERT: A 415 SER cc_start: 0.8530 (p) cc_final: 0.7990 (p) REVERT: A 459 MET cc_start: 0.7634 (mtt) cc_final: 0.7053 (mtt) REVERT: A 483 TYR cc_start: 0.8557 (m-80) cc_final: 0.8256 (m-10) REVERT: A 505 ASP cc_start: 0.8319 (m-30) cc_final: 0.8106 (m-30) REVERT: A 517 GLU cc_start: 0.8920 (tt0) cc_final: 0.8501 (tm-30) REVERT: A 657 ASP cc_start: 0.7810 (p0) cc_final: 0.7540 (p0) REVERT: A 1023 CYS cc_start: 0.7976 (t) cc_final: 0.7774 (t) REVERT: A 1165 GLN cc_start: 0.8035 (mp10) cc_final: 0.7572 (tm-30) REVERT: D 90 LEU cc_start: 0.9115 (mt) cc_final: 0.8883 (mt) REVERT: D 119 MET cc_start: 0.8546 (mmp) cc_final: 0.7889 (mmm) REVERT: E 724 GLU cc_start: 0.8331 (pm20) cc_final: 0.8100 (pm20) REVERT: B 52 CYS cc_start: 0.8096 (p) cc_final: 0.7764 (t) REVERT: B 232 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8595 (mt-10) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.1108 time to fit residues: 27.6662 Evaluate side-chains 136 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 38 optimal weight: 0.0070 chunk 140 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 143 optimal weight: 0.0970 chunk 117 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 197 ASN A 490 HIS A1165 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.082233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.066350 restraints weight = 64894.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.067944 restraints weight = 42035.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.069015 restraints weight = 31261.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.069682 restraints weight = 25516.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.070160 restraints weight = 22309.981| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12743 Z= 0.119 Angle : 0.738 27.402 17232 Z= 0.317 Chirality : 0.044 0.182 1896 Planarity : 0.004 0.046 2200 Dihedral : 5.004 47.240 1661 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.07 % Allowed : 1.16 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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 (0.21), residues: 1517 helix: 0.69 (0.21), residues: 566 sheet: -0.38 (0.33), residues: 253 loop : -0.76 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1173 TYR 0.022 0.002 TYR A 416 PHE 0.017 0.001 PHE B 288 TRP 0.043 0.002 TRP B 284 HIS 0.004 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00256 (12739) covalent geometry : angle 0.62080 (17220) hydrogen bonds : bond 0.04091 ( 401) hydrogen bonds : angle 5.06585 ( 1146) metal coordination : bond 0.00394 ( 4) metal coordination : angle 15.14334 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.473 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: symmetry clash REVERT: A 135 TYR cc_start: 0.7976 (t80) cc_final: 0.7216 (t80) REVERT: A 186 LYS cc_start: 0.8792 (tttp) cc_final: 0.8238 (tptt) REVERT: A 193 PHE cc_start: 0.7401 (m-10) cc_final: 0.7132 (m-10) REVERT: A 459 MET cc_start: 0.7407 (mtt) cc_final: 0.6906 (mtt) REVERT: A 483 TYR cc_start: 0.8483 (m-80) cc_final: 0.8198 (m-10) REVERT: A 517 GLU cc_start: 0.8849 (tt0) cc_final: 0.8472 (tm-30) REVERT: A 637 TYR cc_start: 0.8021 (m-10) cc_final: 0.7699 (m-80) REVERT: A 657 ASP cc_start: 0.7960 (p0) cc_final: 0.7451 (p0) REVERT: A 835 MET cc_start: 0.8967 (mpp) cc_final: 0.8684 (mpp) REVERT: A 846 MET cc_start: 0.8621 (tpp) cc_final: 0.8303 (tpp) REVERT: A 953 MET cc_start: 0.8357 (tpt) cc_final: 0.8144 (tpp) REVERT: A 1165 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: D 90 LEU cc_start: 0.8956 (mt) cc_final: 0.8734 (mt) REVERT: B 16 LYS cc_start: 0.9023 (mttm) cc_final: 0.8711 (mmpt) REVERT: B 52 CYS cc_start: 0.7906 (p) cc_final: 0.7666 (t) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.1133 time to fit residues: 30.2831 Evaluate side-chains 143 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 54 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 HIS A1165 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** 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 = 0.3694 r_free = 0.3694 target = 0.080561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064840 restraints weight = 66435.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066333 restraints weight = 44032.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067330 restraints weight = 33167.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.067878 restraints weight = 27382.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.068325 restraints weight = 24306.178| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12743 Z= 0.169 Angle : 0.773 28.468 17232 Z= 0.331 Chirality : 0.044 0.208 1896 Planarity : 0.005 0.050 2200 Dihedral : 5.005 44.210 1661 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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 (0.21), residues: 1517 helix: 0.62 (0.21), residues: 566 sheet: -0.45 (0.33), residues: 255 loop : -0.67 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1173 TYR 0.021 0.002 TYR A 770 PHE 0.016 0.002 PHE B 288 TRP 0.019 0.002 TRP B 284 HIS 0.004 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00366 (12739) covalent geometry : angle 0.64649 (17220) hydrogen bonds : bond 0.04080 ( 401) hydrogen bonds : angle 5.10465 ( 1146) metal coordination : bond 0.00912 ( 4) metal coordination : angle 16.06445 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.622 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: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.8067 (t80) cc_final: 0.7307 (t80) REVERT: A 186 LYS cc_start: 0.8893 (tttp) cc_final: 0.8337 (tptt) REVERT: A 193 PHE cc_start: 0.7507 (m-10) cc_final: 0.7192 (m-10) REVERT: A 459 MET cc_start: 0.7494 (mtt) cc_final: 0.6977 (mtt) REVERT: A 483 TYR cc_start: 0.8475 (m-80) cc_final: 0.8236 (m-10) REVERT: A 517 GLU cc_start: 0.8796 (tt0) cc_final: 0.8320 (tm-30) REVERT: A 521 MET cc_start: 0.9365 (mtt) cc_final: 0.8370 (mtt) REVERT: A 657 ASP cc_start: 0.8001 (p0) cc_final: 0.7672 (p0) REVERT: A 953 MET cc_start: 0.8333 (tpt) cc_final: 0.7995 (tpt) REVERT: A 1165 GLN cc_start: 0.8212 (mp10) cc_final: 0.7981 (tm-30) REVERT: D 90 LEU cc_start: 0.9043 (mt) cc_final: 0.8829 (mt) REVERT: D 119 MET cc_start: 0.8434 (mmp) cc_final: 0.7694 (mmm) REVERT: B 232 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8617 (mt-10) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1096 time to fit residues: 29.1851 Evaluate side-chains 141 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 0.7980 chunk 142 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 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 = 0.3712 r_free = 0.3712 target = 0.081425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.065557 restraints weight = 66041.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067120 restraints weight = 42741.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.068161 restraints weight = 31795.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.068833 restraints weight = 26027.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.069192 restraints weight = 22820.248| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12743 Z= 0.136 Angle : 0.745 26.921 17232 Z= 0.320 Chirality : 0.044 0.168 1896 Planarity : 0.004 0.046 2200 Dihedral : 4.898 42.026 1661 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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 (0.22), residues: 1517 helix: 0.69 (0.21), residues: 568 sheet: -0.45 (0.33), residues: 255 loop : -0.66 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1173 TYR 0.035 0.002 TYR A 343 PHE 0.015 0.001 PHE B 288 TRP 0.012 0.001 TRP A1026 HIS 0.004 0.001 HIS A1033 Details of bonding type rmsd covalent geometry : bond 0.00296 (12739) covalent geometry : angle 0.62952 (17220) hydrogen bonds : bond 0.03914 ( 401) hydrogen bonds : angle 5.07789 ( 1146) metal coordination : bond 0.00642 ( 4) metal coordination : angle 15.08234 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.496 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: A 135 TYR cc_start: 0.7911 (t80) cc_final: 0.7276 (t80) REVERT: A 186 LYS cc_start: 0.8859 (tttp) cc_final: 0.8307 (tptt) REVERT: A 193 PHE cc_start: 0.7478 (m-10) cc_final: 0.7229 (m-10) REVERT: A 459 MET cc_start: 0.7493 (mtt) cc_final: 0.7041 (mtt) REVERT: A 483 TYR cc_start: 0.8539 (m-80) cc_final: 0.8269 (m-10) REVERT: A 517 GLU cc_start: 0.8773 (tt0) cc_final: 0.8330 (tm-30) REVERT: A 521 MET cc_start: 0.9345 (mtt) cc_final: 0.8516 (mtt) REVERT: A 657 ASP cc_start: 0.7905 (p0) cc_final: 0.7515 (p0) REVERT: A 835 MET cc_start: 0.8974 (mpp) cc_final: 0.8724 (mpp) REVERT: A 953 MET cc_start: 0.8326 (tpt) cc_final: 0.7974 (tpt) REVERT: D 90 LEU cc_start: 0.8989 (mt) cc_final: 0.8775 (mt) REVERT: B 16 LYS cc_start: 0.9029 (mttm) cc_final: 0.8765 (mmpt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1018 time to fit residues: 27.0146 Evaluate side-chains 138 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 0.0010 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 129 optimal weight: 0.0000 chunk 114 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN D 16 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** 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 = 0.3737 r_free = 0.3737 target = 0.082604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.066714 restraints weight = 64819.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.068279 restraints weight = 42402.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.069335 restraints weight = 31606.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.070009 restraints weight = 25989.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.070502 restraints weight = 22736.860| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12743 Z= 0.113 Angle : 0.708 24.774 17232 Z= 0.308 Chirality : 0.043 0.183 1896 Planarity : 0.004 0.046 2200 Dihedral : 4.713 41.835 1661 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.07 % Allowed : 0.07 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -0.03 (0.22), residues: 1517 helix: 0.85 (0.21), residues: 560 sheet: -0.31 (0.34), residues: 241 loop : -0.53 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1173 TYR 0.023 0.001 TYR A 343 PHE 0.019 0.001 PHE B 288 TRP 0.012 0.001 TRP A1026 HIS 0.004 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00244 (12739) covalent geometry : angle 0.61246 (17220) hydrogen bonds : bond 0.03715 ( 401) hydrogen bonds : angle 4.97311 ( 1146) metal coordination : bond 0.00283 ( 4) metal coordination : angle 13.48884 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7945 (t80) cc_final: 0.7466 (t80) REVERT: A 186 LYS cc_start: 0.8809 (tttp) cc_final: 0.8260 (tptt) REVERT: A 193 PHE cc_start: 0.7360 (m-10) cc_final: 0.7114 (m-10) REVERT: A 459 MET cc_start: 0.7442 (mtt) cc_final: 0.7038 (mtt) REVERT: A 517 GLU cc_start: 0.8736 (tt0) cc_final: 0.8479 (tm-30) REVERT: A 657 ASP cc_start: 0.7900 (p0) cc_final: 0.7455 (p0) REVERT: A 835 MET cc_start: 0.8954 (mpp) cc_final: 0.8687 (mpp) REVERT: A 879 ILE cc_start: 0.9209 (mt) cc_final: 0.8877 (mm) REVERT: A 953 MET cc_start: 0.8310 (tpt) cc_final: 0.7919 (tpt) REVERT: D 90 LEU cc_start: 0.8971 (mt) cc_final: 0.8759 (mt) REVERT: D 119 MET cc_start: 0.8596 (mmp) cc_final: 0.8380 (mmp) REVERT: B 16 LYS cc_start: 0.8995 (mttm) cc_final: 0.8709 (mmpt) REVERT: B 232 GLU cc_start: 0.8855 (pt0) cc_final: 0.8525 (pp20) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1072 time to fit residues: 28.3772 Evaluate side-chains 140 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 0.0170 chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 0.1980 chunk 5 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 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 = 0.3746 r_free = 0.3746 target = 0.083133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.067367 restraints weight = 64539.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.068963 restraints weight = 42070.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.070011 restraints weight = 31216.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.070711 restraints weight = 25469.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.071172 restraints weight = 22261.476| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 12743 Z= 0.107 Angle : 0.698 23.820 17232 Z= 0.303 Chirality : 0.043 0.172 1896 Planarity : 0.004 0.044 2200 Dihedral : 4.612 40.050 1661 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.08 (0.22), residues: 1517 helix: 0.96 (0.22), residues: 561 sheet: -0.33 (0.35), residues: 242 loop : -0.45 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1173 TYR 0.019 0.001 TYR A 343 PHE 0.020 0.001 PHE D 45 TRP 0.012 0.001 TRP A1026 HIS 0.010 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00235 (12739) covalent geometry : angle 0.60965 (17220) hydrogen bonds : bond 0.03616 ( 401) hydrogen bonds : angle 4.94160 ( 1146) metal coordination : bond 0.00268 ( 4) metal coordination : angle 12.91459 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2154.87 seconds wall clock time: 38 minutes 5.91 seconds (2285.91 seconds total)