Starting phenix.real_space_refine on Thu Jul 2 02:04:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqc_62500/07_2026/9kqc_62500_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqc_62500/07_2026/9kqc_62500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kqc_62500/07_2026/9kqc_62500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqc_62500/07_2026/9kqc_62500.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqc_62500/07_2026/9kqc_62500_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqc_62500/07_2026/9kqc_62500_neut.cif" } resolution = 3.36 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 960 atoms to isotropic. 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 Mn 1 7.51 5 P 2 5.49 5 S 30 5.16 5 C 3193 2.51 5 N 800 2.21 5 O 898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 4924 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4077 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 13, 'TRANS': 486} Chain breaks: 1 Chain: "B" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'UD1': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'UD1:plan-1': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.22, per 1000 atoms: 0.25 Number of scatterers: 4924 At special positions: 0 Unit cell: (72.68, 67.16, 120.52, 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) Mn 1 24.99 S 30 16.00 P 2 15.00 O 898 8.00 N 800 7.00 C 3193 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 83 " distance=2.03 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 107.9 milliseconds 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1142 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 5 sheets defined 57.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 38 through 74 removed outlier: 3.754A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 108 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.518A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.720A pdb=" N THR A 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.714A pdb=" N ASP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.886A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 221' Processing helix chain 'A' and resid 238 through 254 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 276 through 289 removed outlier: 4.747A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 331 through 358 removed outlier: 4.273A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TRP A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 364 through 392 Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.867A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 450 removed outlier: 3.762A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix removed outlier: 4.676A pdb=" N PHE A 450 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 497 removed outlier: 3.612A pdb=" N GLN A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N THR A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 534 Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.674A pdb=" N LYS A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 8.636A pdb=" N ILE A 168 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 116 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE A 170 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS A 118 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL A 84 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A 115 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE A 200 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A 87 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 206 removed outlier: 7.554A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 4 removed outlier: 3.528A pdb=" N VAL B 23 " --> pdb=" O GLU B 4 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 9 through 13 removed outlier: 3.605A pdb=" N LYS B 107 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR B 80 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE B 38 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS B 82 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TRP B 36 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS B 84 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR B 34 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR B 86 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 13 removed outlier: 3.605A pdb=" N LYS B 107 " --> pdb=" O LYS B 12 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1501 1.34 - 1.46: 1082 1.46 - 1.58: 2417 1.58 - 1.69: 4 1.69 - 1.81: 44 Bond restraints: 5048 Sorted by residual: bond pdb=" CA ASP A 301 " pdb=" C ASP A 301 " ideal model delta sigma weight residual 1.524 1.487 0.036 1.29e-02 6.01e+03 7.98e+00 bond pdb=" C4 UD1 A 601 " pdb=" C5 UD1 A 601 " ideal model delta sigma weight residual 1.441 1.389 0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C ASP A 221 " pdb=" O ASP A 221 " ideal model delta sigma weight residual 1.249 1.228 0.021 8.50e-03 1.38e+04 6.17e+00 bond pdb=" C4 UD1 A 601 " pdb=" N3 UD1 A 601 " ideal model delta sigma weight residual 1.386 1.337 0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" O1' UD1 A 601 " pdb=" PB UD1 A 601 " ideal model delta sigma weight residual 1.658 1.609 0.049 2.00e-02 2.50e+03 5.98e+00 ... (remaining 5043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 6594 2.04 - 4.09: 208 4.09 - 6.13: 41 6.13 - 8.17: 16 8.17 - 10.21: 3 Bond angle restraints: 6862 Sorted by residual: angle pdb=" N ASP A 301 " pdb=" CA ASP A 301 " pdb=" C ASP A 301 " ideal model delta sigma weight residual 111.36 104.10 7.26 1.09e+00 8.42e-01 4.44e+01 angle pdb=" N LEU A 212 " pdb=" CA LEU A 212 " pdb=" C LEU A 212 " ideal model delta sigma weight residual 111.33 103.61 7.72 1.21e+00 6.83e-01 4.07e+01 angle pdb=" CA LYS A 177 " pdb=" C LYS A 177 " pdb=" N ARG A 178 " ideal model delta sigma weight residual 119.46 116.15 3.31 6.10e-01 2.69e+00 2.95e+01 angle pdb=" N ARG A 175 " pdb=" CA ARG A 175 " pdb=" C ARG A 175 " ideal model delta sigma weight residual 113.88 108.13 5.75 1.23e+00 6.61e-01 2.19e+01 angle pdb=" N GLY B 15 " pdb=" CA GLY B 15 " pdb=" C GLY B 15 " ideal model delta sigma weight residual 113.18 102.97 10.21 2.37e+00 1.78e-01 1.86e+01 ... (remaining 6857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 2485 17.87 - 35.75: 342 35.75 - 53.62: 89 53.62 - 71.50: 31 71.50 - 89.37: 6 Dihedral angle restraints: 2953 sinusoidal: 1169 harmonic: 1784 Sorted by residual: dihedral pdb=" CA GLY B 15 " pdb=" C GLY B 15 " pdb=" N GLU B 16 " pdb=" CA GLU B 16 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA GLY A 146 " pdb=" C GLY A 146 " pdb=" N VAL A 147 " pdb=" CA VAL A 147 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 83 " pdb=" CB CYS B 83 " ideal model delta sinusoidal sigma weight residual 93.00 65.55 27.45 1 1.00e+01 1.00e-02 1.08e+01 ... (remaining 2950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 631 0.057 - 0.115: 114 0.115 - 0.172: 15 0.172 - 0.229: 2 0.229 - 0.286: 1 Chirality restraints: 763 Sorted by residual: chirality pdb=" C1B UD1 A 601 " pdb=" C2B UD1 A 601 " pdb=" N1 UD1 A 601 " pdb=" O4B UD1 A 601 " both_signs ideal model delta sigma weight residual False 2.20 2.49 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB THR A 400 " pdb=" CA THR A 400 " pdb=" OG1 THR A 400 " pdb=" CG2 THR A 400 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CG LEU A 218 " pdb=" CB LEU A 218 " pdb=" CD1 LEU A 218 " pdb=" CD2 LEU A 218 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 760 not shown) Planarity restraints: 838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 93 " -0.032 2.00e-02 2.50e+03 2.33e-02 1.35e+01 pdb=" CG TRP B 93 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP B 93 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 93 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 93 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 93 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 93 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 93 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 93 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 93 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 303 " -0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ARG A 303 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG A 303 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG A 304 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 300 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C GLY A 300 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY A 300 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP A 301 " 0.016 2.00e-02 2.50e+03 ... (remaining 835 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 298 2.72 - 3.26: 5579 3.26 - 3.81: 9292 3.81 - 4.35: 10422 4.35 - 4.90: 16885 Nonbonded interactions: 42476 Sorted by model distance: nonbonded pdb=" OE2 GLU A 93 " pdb="MN MN A 602 " model vdw 2.172 3.060 nonbonded pdb=" CA GLY A 90 " pdb=" O2' UD1 A 601 " model vdw 2.218 3.440 nonbonded pdb=" N GLU A 544 " pdb=" OE1 GLU A 544 " model vdw 2.253 3.120 nonbonded pdb=" NH2 ARG A 106 " pdb=" O VAL A 137 " model vdw 2.258 3.120 nonbonded pdb=" O GLU A 349 " pdb=" OG1 THR A 353 " model vdw 2.324 3.040 ... (remaining 42471 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: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.390 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 0.052 5050 Z= 0.288 Angle : 0.899 10.213 6866 Z= 0.525 Chirality : 0.045 0.286 763 Planarity : 0.004 0.040 838 Dihedral : 18.533 89.370 1805 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 1.00 % Allowed : 5.32 % Favored : 93.68 % Rotamer: Outliers : 8.51 % Allowed : 20.23 % Favored : 71.27 % 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: 0.10 (0.36), residues: 601 helix: 0.68 (0.30), residues: 320 sheet: 0.73 (0.54), residues: 104 loop : -1.37 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 334 TYR 0.033 0.002 TYR A 414 PHE 0.021 0.001 PHE A 369 TRP 0.060 0.002 TRP B 93 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.29 ( 5048) covalent geometry : angle 0.89826 / 0.52 ( 6862) SS BOND : bond 0.00333 / 0.17 ( 2) SS BOND : angle 1.38556 / 0.74 ( 4) hydrogen bonds : bond 0.14190 / 9.55 ( 277) hydrogen bonds : angle 6.30767 / 4.68 ( 810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 0.192 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 190 MET cc_start: 0.7784 (mtp) cc_final: 0.7387 (mtp) REVERT: A 206 LEU cc_start: 0.7908 (mm) cc_final: 0.7653 (mm) REVERT: A 224 ILE cc_start: 0.8952 (mt) cc_final: 0.8638 (mt) REVERT: A 266 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: A 311 MET cc_start: 0.8217 (mtt) cc_final: 0.7988 (mpt) REVERT: A 333 MET cc_start: 0.8349 (mmp) cc_final: 0.7670 (mmm) REVERT: A 390 ILE cc_start: 0.8997 (mm) cc_final: 0.8783 (pt) REVERT: A 426 TYR cc_start: 0.8430 (m-80) cc_final: 0.8205 (m-80) REVERT: B 60 ASN cc_start: 0.9251 (t0) cc_final: 0.8997 (t0) outliers start: 45 outliers final: 13 residues processed: 175 average time/residue: 0.0790 time to fit residues: 17.2920 Evaluate side-chains 116 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.0770 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN A 338 GLN A 421 ASN ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 HIS ** 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 = 0.3605 r_free = 0.3605 target = 0.086746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.064980 restraints weight = 16309.964| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 5.16 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5050 Z= 0.143 Angle : 0.667 9.990 6866 Z= 0.333 Chirality : 0.043 0.141 763 Planarity : 0.005 0.053 838 Dihedral : 9.535 102.562 729 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.00 % Favored : 97.84 % Rotamer: Outliers : 6.05 % Allowed : 19.66 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.91 (0.35), residues: 601 helix: 1.40 (0.30), residues: 321 sheet: 0.50 (0.51), residues: 112 loop : -0.78 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 69 TYR 0.023 0.001 TYR A 414 PHE 0.014 0.001 PHE A 53 TRP 0.016 0.001 TRP B 93 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 5048) covalent geometry : angle 0.66705 / 0.33 ( 6862) SS BOND : bond 0.00681 / 0.36 ( 2) SS BOND : angle 1.05458 / 0.56 ( 4) hydrogen bonds : bond 0.04059 / 2.78 ( 277) hydrogen bonds : angle 4.69122 / 3.54 ( 810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8374 (mtp) cc_final: 0.8132 (mtp) REVERT: A 191 ASP cc_start: 0.9075 (t0) cc_final: 0.8782 (t0) REVERT: A 230 GLU cc_start: 0.8646 (tm-30) cc_final: 0.7944 (tm-30) REVERT: A 331 ASN cc_start: 0.8486 (t0) cc_final: 0.8082 (t0) REVERT: A 356 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8678 (p) REVERT: A 376 MET cc_start: 0.8501 (tmm) cc_final: 0.8214 (tmm) REVERT: A 390 ILE cc_start: 0.9051 (mm) cc_final: 0.8810 (pt) REVERT: A 397 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8618 (mp10) REVERT: A 474 LYS cc_start: 0.9030 (mtmt) cc_final: 0.8567 (mmtt) REVERT: B 12 LYS cc_start: 0.7652 (ttpp) cc_final: 0.7083 (tmmt) REVERT: B 16 GLU cc_start: 0.9403 (mt-10) cc_final: 0.9138 (mp0) REVERT: B 93 TRP cc_start: 0.6531 (OUTLIER) cc_final: 0.5772 (t60) outliers start: 32 outliers final: 20 residues processed: 136 average time/residue: 0.0685 time to fit residues: 12.0810 Evaluate side-chains 118 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 93 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 HIS A 281 ASN B 1 GLN ** B 82 HIS ** 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 = 0.3567 r_free = 0.3567 target = 0.084786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.062897 restraints weight = 16153.397| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 5.05 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5050 Z= 0.143 Angle : 0.621 10.414 6866 Z= 0.311 Chirality : 0.042 0.152 763 Planarity : 0.004 0.049 838 Dihedral : 7.679 59.178 711 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.00 % Favored : 97.84 % Rotamer: Outliers : 6.81 % Allowed : 20.98 % Favored : 72.21 % 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: 1.07 (0.35), residues: 601 helix: 1.55 (0.29), residues: 321 sheet: 0.48 (0.51), residues: 111 loop : -0.69 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 178 TYR 0.019 0.001 TYR A 414 PHE 0.013 0.001 PHE A 49 TRP 0.018 0.001 TRP B 93 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5048) covalent geometry : angle 0.62019 / 0.31 ( 6862) SS BOND : bond 0.00223 / 0.11 ( 2) SS BOND : angle 1.60387 / 0.84 ( 4) hydrogen bonds : bond 0.03829 / 2.56 ( 277) hydrogen bonds : angle 4.51998 / 3.40 ( 810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.9018 (tp) REVERT: A 178 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7509 (mtp85) REVERT: A 191 ASP cc_start: 0.9226 (t0) cc_final: 0.8882 (t0) REVERT: A 230 GLU cc_start: 0.8657 (tm-30) cc_final: 0.7944 (tm-30) REVERT: A 236 THR cc_start: 0.9001 (p) cc_final: 0.8717 (t) REVERT: A 282 GLU cc_start: 0.9449 (tp30) cc_final: 0.8789 (tt0) REVERT: A 331 ASN cc_start: 0.8538 (t0) cc_final: 0.8171 (t0) REVERT: A 356 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8650 (p) REVERT: A 376 MET cc_start: 0.8530 (tmm) cc_final: 0.8298 (tmm) REVERT: A 390 ILE cc_start: 0.9115 (mm) cc_final: 0.8844 (pt) REVERT: A 397 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8643 (mp10) REVERT: B 12 LYS cc_start: 0.7967 (ttpp) cc_final: 0.7567 (ttpt) REVERT: B 16 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8985 (mp0) REVERT: B 54 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6865 (mtp-110) outliers start: 36 outliers final: 19 residues processed: 131 average time/residue: 0.0664 time to fit residues: 11.3858 Evaluate side-chains 116 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 93 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN B 1 GLN ** B 82 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 = 0.3512 r_free = 0.3512 target = 0.081873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.059890 restraints weight = 16006.546| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.83 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5050 Z= 0.176 Angle : 0.622 7.856 6866 Z= 0.317 Chirality : 0.043 0.148 763 Planarity : 0.004 0.053 838 Dihedral : 7.513 59.530 708 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.16 % Favored : 97.67 % Rotamer: Outliers : 6.62 % Allowed : 21.93 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.35), residues: 601 helix: 1.71 (0.30), residues: 317 sheet: 0.52 (0.51), residues: 111 loop : -0.58 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 178 TYR 0.018 0.002 TYR A 414 PHE 0.017 0.001 PHE A 476 TRP 0.021 0.001 TRP B 93 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 5048) covalent geometry : angle 0.62148 / 0.32 ( 6862) SS BOND : bond 0.00153 / 0.08 ( 2) SS BOND : angle 1.40497 / 0.74 ( 4) hydrogen bonds : bond 0.03864 / 2.52 ( 277) hydrogen bonds : angle 4.46167 / 3.35 ( 810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7721 (mtp85) REVERT: A 190 MET cc_start: 0.8757 (mtp) cc_final: 0.8549 (mtp) REVERT: A 191 ASP cc_start: 0.9387 (t0) cc_final: 0.9043 (t0) REVERT: A 201 ASP cc_start: 0.8601 (m-30) cc_final: 0.7886 (t0) REVERT: A 230 GLU cc_start: 0.8667 (tm-30) cc_final: 0.7944 (tm-30) REVERT: A 236 THR cc_start: 0.9155 (p) cc_final: 0.8874 (t) REVERT: A 266 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: A 282 GLU cc_start: 0.9442 (tp30) cc_final: 0.8782 (tm-30) REVERT: A 331 ASN cc_start: 0.8503 (t0) cc_final: 0.8190 (t0) REVERT: A 376 MET cc_start: 0.8583 (tmm) cc_final: 0.8272 (tmm) REVERT: A 390 ILE cc_start: 0.9208 (mm) cc_final: 0.8910 (pt) REVERT: B 1 GLN cc_start: 0.8599 (mt0) cc_final: 0.8343 (mt0) REVERT: B 16 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8762 (mp0) REVERT: B 45 LYS cc_start: 0.9456 (tppt) cc_final: 0.9247 (tptp) outliers start: 35 outliers final: 24 residues processed: 126 average time/residue: 0.0720 time to fit residues: 11.6654 Evaluate side-chains 115 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN ** B 82 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 = 0.3456 r_free = 0.3456 target = 0.079425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.056988 restraints weight = 16316.492| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.86 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5050 Z= 0.196 Angle : 0.640 10.122 6866 Z= 0.327 Chirality : 0.044 0.159 763 Planarity : 0.005 0.057 838 Dihedral : 7.443 59.072 708 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.83 % Favored : 98.00 % Rotamer: Outliers : 7.75 % Allowed : 21.74 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.35), residues: 601 helix: 1.76 (0.30), residues: 317 sheet: 0.34 (0.50), residues: 110 loop : -0.56 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 25 TYR 0.017 0.002 TYR A 414 PHE 0.012 0.001 PHE A 53 TRP 0.020 0.001 TRP B 93 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 ( 5048) covalent geometry : angle 0.63973 / 0.33 ( 6862) SS BOND : bond 0.00198 / 0.10 ( 2) SS BOND : angle 1.02321 / 0.52 ( 4) hydrogen bonds : bond 0.03849 / 2.51 ( 277) hydrogen bonds : angle 4.53433 / 3.41 ( 810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7713 (mtp85) REVERT: A 190 MET cc_start: 0.8723 (mtp) cc_final: 0.8518 (mtp) REVERT: A 191 ASP cc_start: 0.9448 (t0) cc_final: 0.9137 (t0) REVERT: A 230 GLU cc_start: 0.8668 (tm-30) cc_final: 0.7927 (tm-30) REVERT: A 266 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: A 282 GLU cc_start: 0.9430 (tp30) cc_final: 0.8895 (tm-30) REVERT: A 348 ARG cc_start: 0.8595 (ttp-170) cc_final: 0.8296 (ttp-170) REVERT: A 376 MET cc_start: 0.8590 (tmm) cc_final: 0.8201 (tmm) REVERT: A 475 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8735 (pm20) REVERT: B 16 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8887 (mp0) REVERT: B 87 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8535 (p) outliers start: 41 outliers final: 28 residues processed: 123 average time/residue: 0.0669 time to fit residues: 10.6917 Evaluate side-chains 117 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 ASN A 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.080961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.058703 restraints weight = 16277.236| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.95 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5050 Z= 0.124 Angle : 0.621 9.365 6866 Z= 0.310 Chirality : 0.042 0.160 763 Planarity : 0.004 0.054 838 Dihedral : 7.291 59.984 708 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.83 % Favored : 98.00 % Rotamer: Outliers : 7.56 % Allowed : 22.31 % Favored : 70.13 % 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: 1.29 (0.34), residues: 601 helix: 1.83 (0.29), residues: 317 sheet: 0.44 (0.51), residues: 106 loop : -0.62 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 74 TYR 0.016 0.001 TYR A 373 PHE 0.011 0.001 PHE A 49 TRP 0.016 0.001 TRP B 93 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 5048) covalent geometry : angle 0.62050 / 0.31 ( 6862) SS BOND : bond 0.00222 / 0.12 ( 2) SS BOND : angle 0.86447 / 0.45 ( 4) hydrogen bonds : bond 0.03727 / 2.44 ( 277) hydrogen bonds : angle 4.40138 / 3.31 ( 810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7772 (mtp85) REVERT: A 190 MET cc_start: 0.8816 (mtp) cc_final: 0.8543 (mtp) REVERT: A 191 ASP cc_start: 0.9445 (t0) cc_final: 0.9148 (t0) REVERT: A 230 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 266 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: A 282 GLU cc_start: 0.9442 (tp30) cc_final: 0.8885 (tm-30) REVERT: A 331 ASN cc_start: 0.8567 (t0) cc_final: 0.8292 (t0) REVERT: A 376 MET cc_start: 0.8555 (tmm) cc_final: 0.8136 (tmm) REVERT: A 390 ILE cc_start: 0.8549 (tt) cc_final: 0.8095 (pt) REVERT: B 12 LYS cc_start: 0.7470 (tttt) cc_final: 0.6972 (tmtt) REVERT: B 16 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8640 (mp0) REVERT: B 18 LEU cc_start: 0.9364 (tt) cc_final: 0.8938 (mm) REVERT: B 87 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8478 (p) REVERT: B 93 TRP cc_start: 0.6822 (OUTLIER) cc_final: 0.6285 (t60) outliers start: 40 outliers final: 30 residues processed: 127 average time/residue: 0.0689 time to fit residues: 11.4537 Evaluate side-chains 118 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 ASN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.080406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058579 restraints weight = 15854.313| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.80 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5050 Z= 0.137 Angle : 0.641 9.590 6866 Z= 0.322 Chirality : 0.042 0.169 763 Planarity : 0.004 0.054 838 Dihedral : 7.194 58.925 708 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.66 % Favored : 98.17 % Rotamer: Outliers : 7.37 % Allowed : 22.12 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.34), residues: 601 helix: 1.75 (0.29), residues: 317 sheet: 0.49 (0.51), residues: 107 loop : -0.60 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 74 TYR 0.015 0.001 TYR A 414 PHE 0.011 0.001 PHE A 49 TRP 0.016 0.001 TRP B 93 HIS 0.010 0.002 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 5048) covalent geometry : angle 0.64077 / 0.32 ( 6862) SS BOND : bond 0.00229 / 0.12 ( 2) SS BOND : angle 0.78259 / 0.41 ( 4) hydrogen bonds : bond 0.03672 / 2.41 ( 277) hydrogen bonds : angle 4.37181 / 3.28 ( 810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7769 (mtp85) REVERT: A 190 MET cc_start: 0.8835 (mtp) cc_final: 0.8493 (mtp) REVERT: A 191 ASP cc_start: 0.9451 (t0) cc_final: 0.9118 (t0) REVERT: A 230 GLU cc_start: 0.8631 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 266 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: A 282 GLU cc_start: 0.9453 (tp30) cc_final: 0.8897 (tm-30) REVERT: A 331 ASN cc_start: 0.8541 (t0) cc_final: 0.8272 (t0) REVERT: A 376 MET cc_start: 0.8551 (tmm) cc_final: 0.8120 (tmm) REVERT: A 390 ILE cc_start: 0.8577 (tt) cc_final: 0.8144 (pt) REVERT: A 479 THR cc_start: 0.9545 (m) cc_final: 0.9341 (t) REVERT: B 12 LYS cc_start: 0.7473 (tttt) cc_final: 0.7024 (tmtt) REVERT: B 16 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8550 (mp0) REVERT: B 18 LEU cc_start: 0.9333 (tt) cc_final: 0.8908 (mm) REVERT: B 26 ASP cc_start: 0.9035 (m-30) cc_final: 0.8635 (t0) REVERT: B 87 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8483 (p) REVERT: B 93 TRP cc_start: 0.6819 (OUTLIER) cc_final: 0.6305 (t60) outliers start: 39 outliers final: 27 residues processed: 124 average time/residue: 0.0689 time to fit residues: 11.3135 Evaluate side-chains 115 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.081188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.059700 restraints weight = 16231.634| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.78 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5050 Z= 0.123 Angle : 0.639 9.874 6866 Z= 0.323 Chirality : 0.043 0.168 763 Planarity : 0.004 0.055 838 Dihedral : 7.088 59.488 707 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.66 % Favored : 98.17 % Rotamer: Outliers : 6.81 % Allowed : 22.50 % Favored : 70.70 % 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: 1.24 (0.34), residues: 601 helix: 1.72 (0.29), residues: 317 sheet: 0.58 (0.51), residues: 107 loop : -0.62 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 74 TYR 0.019 0.001 TYR A 373 PHE 0.011 0.001 PHE A 49 TRP 0.015 0.001 TRP B 93 HIS 0.007 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 5048) covalent geometry : angle 0.63887 / 0.32 ( 6862) SS BOND : bond 0.00256 / 0.13 ( 2) SS BOND : angle 0.69853 / 0.37 ( 4) hydrogen bonds : bond 0.03677 / 2.44 ( 277) hydrogen bonds : angle 4.33315 / 3.26 ( 810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7771 (mtp85) REVERT: A 190 MET cc_start: 0.8846 (mtp) cc_final: 0.8381 (mmm) REVERT: A 191 ASP cc_start: 0.9458 (t0) cc_final: 0.9145 (t0) REVERT: A 230 GLU cc_start: 0.8594 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 266 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: A 282 GLU cc_start: 0.9453 (tp30) cc_final: 0.8899 (tm-30) REVERT: A 348 ARG cc_start: 0.8558 (ttp-170) cc_final: 0.8239 (ttp-170) REVERT: A 390 ILE cc_start: 0.8575 (tt) cc_final: 0.8147 (pt) REVERT: A 438 MET cc_start: 0.9077 (mmm) cc_final: 0.8865 (mmm) REVERT: A 479 THR cc_start: 0.9537 (m) cc_final: 0.9326 (t) REVERT: B 12 LYS cc_start: 0.7478 (tttt) cc_final: 0.7038 (tmtt) REVERT: B 16 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8499 (mp0) REVERT: B 18 LEU cc_start: 0.9346 (tt) cc_final: 0.8946 (mm) REVERT: B 87 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8456 (p) REVERT: B 93 TRP cc_start: 0.6818 (OUTLIER) cc_final: 0.6288 (t60) outliers start: 36 outliers final: 26 residues processed: 122 average time/residue: 0.0707 time to fit residues: 11.2707 Evaluate side-chains 114 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.080292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.058261 restraints weight = 15997.451| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.85 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5050 Z= 0.150 Angle : 0.666 9.952 6866 Z= 0.336 Chirality : 0.043 0.171 763 Planarity : 0.004 0.054 838 Dihedral : 6.981 58.809 707 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.00 % Favored : 97.84 % Rotamer: Outliers : 6.99 % Allowed : 22.31 % Favored : 70.70 % 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: 1.29 (0.35), residues: 601 helix: 1.74 (0.29), residues: 317 sheet: 0.62 (0.51), residues: 107 loop : -0.55 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 74 TYR 0.019 0.001 TYR A 373 PHE 0.011 0.001 PHE A 49 TRP 0.016 0.001 TRP B 93 HIS 0.006 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 5048) covalent geometry : angle 0.66589 / 0.34 ( 6862) SS BOND : bond 0.00233 / 0.12 ( 2) SS BOND : angle 0.46927 / 0.23 ( 4) hydrogen bonds : bond 0.03754 / 2.49 ( 277) hydrogen bonds : angle 4.32004 / 3.25 ( 810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7776 (mtp85) REVERT: A 190 MET cc_start: 0.8827 (mtp) cc_final: 0.8356 (mmm) REVERT: A 191 ASP cc_start: 0.9459 (t0) cc_final: 0.9156 (t0) REVERT: A 230 GLU cc_start: 0.8596 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 266 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: A 282 GLU cc_start: 0.9462 (tp30) cc_final: 0.8918 (tm-30) REVERT: A 348 ARG cc_start: 0.8571 (ttp-170) cc_final: 0.8298 (ttp-170) REVERT: B 12 LYS cc_start: 0.7455 (tttt) cc_final: 0.7068 (tmtt) REVERT: B 16 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8495 (mp0) REVERT: B 18 LEU cc_start: 0.9332 (tt) cc_final: 0.8914 (mm) REVERT: B 87 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8439 (p) REVERT: B 93 TRP cc_start: 0.6911 (OUTLIER) cc_final: 0.6301 (t60) REVERT: B 95 ILE cc_start: 0.9033 (mm) cc_final: 0.8314 (mm) outliers start: 37 outliers final: 29 residues processed: 119 average time/residue: 0.0637 time to fit residues: 9.8344 Evaluate side-chains 119 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 50 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.077992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.056069 restraints weight = 16419.400| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.80 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5050 Z= 0.188 Angle : 0.691 9.838 6866 Z= 0.350 Chirality : 0.045 0.175 763 Planarity : 0.004 0.052 838 Dihedral : 6.927 59.933 707 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.33 % Favored : 97.50 % Rotamer: Outliers : 6.62 % Allowed : 22.87 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.35), residues: 601 helix: 1.69 (0.30), residues: 315 sheet: 0.39 (0.51), residues: 109 loop : -0.48 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 74 TYR 0.019 0.002 TYR A 373 PHE 0.011 0.001 PHE A 49 TRP 0.017 0.001 TRP B 93 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 5048) covalent geometry : angle 0.69092 / 0.35 ( 6862) SS BOND : bond 0.00266 / 0.14 ( 2) SS BOND : angle 0.63373 / 0.28 ( 4) hydrogen bonds : bond 0.03930 / 2.61 ( 277) hydrogen bonds : angle 4.38164 / 3.29 ( 810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7804 (mtp85) REVERT: A 190 MET cc_start: 0.8822 (mtp) cc_final: 0.8374 (mmm) REVERT: A 191 ASP cc_start: 0.9488 (t0) cc_final: 0.9203 (t0) REVERT: A 230 GLU cc_start: 0.8556 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 266 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: A 282 GLU cc_start: 0.9470 (tp30) cc_final: 0.8947 (tm-30) REVERT: B 12 LYS cc_start: 0.7476 (tttt) cc_final: 0.7109 (tmtt) REVERT: B 16 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8491 (mp0) REVERT: B 18 LEU cc_start: 0.9324 (tt) cc_final: 0.8920 (mm) REVERT: B 87 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8425 (p) REVERT: B 93 TRP cc_start: 0.7067 (OUTLIER) cc_final: 0.6459 (t60) REVERT: B 95 ILE cc_start: 0.9141 (mm) cc_final: 0.8461 (mm) outliers start: 35 outliers final: 30 residues processed: 113 average time/residue: 0.0695 time to fit residues: 10.2638 Evaluate side-chains 115 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.0870 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.079992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.058245 restraints weight = 16041.241| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.78 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5050 Z= 0.133 Angle : 0.679 10.002 6866 Z= 0.338 Chirality : 0.043 0.174 763 Planarity : 0.004 0.055 838 Dihedral : 6.815 58.929 707 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.66 % Favored : 98.17 % Rotamer: Outliers : 5.67 % Allowed : 24.20 % Favored : 70.13 % 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: 1.17 (0.34), residues: 601 helix: 1.67 (0.29), residues: 315 sheet: 0.43 (0.50), residues: 107 loop : -0.54 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 74 TYR 0.019 0.001 TYR A 373 PHE 0.012 0.001 PHE A 450 TRP 0.013 0.001 TRP B 93 HIS 0.006 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5048) covalent geometry : angle 0.67912 / 0.34 ( 6862) SS BOND : bond 0.00271 / 0.14 ( 2) SS BOND : angle 0.48775 / 0.23 ( 4) hydrogen bonds : bond 0.03883 / 2.60 ( 277) hydrogen bonds : angle 4.33478 / 3.26 ( 810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1300.22 seconds wall clock time: 23 minutes 8.64 seconds (1388.64 seconds total)