Starting phenix.real_space_refine on Thu Jun 5 08:02:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqc_62500/06_2025/9kqc_62500_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqc_62500/06_2025/9kqc_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_62500/06_2025/9kqc_62500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqc_62500/06_2025/9kqc_62500.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqc_62500/06_2025/9kqc_62500_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqc_62500/06_2025/9kqc_62500_neut.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 26 Unusual residues: {' MN': 1, 'UD1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 4.87, per 1000 atoms: 0.99 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: 1.33 Conformation dependent library (CDL) restraints added in 559.5 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: 0.51 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: 1.42 Time building geometry restraints manager: 1.55 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 2.320 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: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.390 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 : 23.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.36), 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 TRP 0.060 0.002 TRP B 93 HIS 0.002 0.001 HIS A 195 PHE 0.021 0.001 PHE A 369 TYR 0.033 0.002 TYR A 414 ARG 0.006 0.001 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.14190 ( 277) hydrogen bonds : angle 6.30767 ( 810) SS BOND : bond 0.00333 ( 2) SS BOND : angle 1.38556 ( 4) covalent geometry : bond 0.00477 ( 5048) covalent geometry : angle 0.89826 ( 6862) *********************** 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 : 0.518 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: 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: 0.8646 (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: 0.9252 (t0) cc_final: 0.8998 (t0) outliers start: 45 outliers final: 13 residues processed: 175 average time/residue: 0.2026 time to fit residues: 43.4921 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 : 0.579 ------------------------------------------------------------------------------- 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 50 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.087086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.065234 restraints weight = 15883.047| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 5.09 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5050 Z= 0.143 Angle : 0.665 9.709 6866 Z= 0.333 Chirality : 0.043 0.190 763 Planarity : 0.004 0.044 838 Dihedral : 9.532 102.257 729 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.16 % Favored : 97.67 % Rotamer: Outliers : 6.43 % Allowed : 20.04 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.35), residues: 601 helix: 1.40 (0.30), residues: 321 sheet: 0.47 (0.51), residues: 112 loop : -0.80 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 93 HIS 0.005 0.001 HIS A 195 PHE 0.014 0.001 PHE A 53 TYR 0.023 0.001 TYR A 414 ARG 0.005 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 277) hydrogen bonds : angle 4.71117 ( 810) SS BOND : bond 0.00220 ( 2) SS BOND : angle 1.34776 ( 4) covalent geometry : bond 0.00317 ( 5048) covalent geometry : angle 0.66410 ( 6862) *********************** 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 146 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8352 (mtp) cc_final: 0.8113 (mtp) REVERT: A 191 ASP cc_start: 0.9048 (t0) cc_final: 0.8759 (t0) REVERT: A 230 GLU cc_start: 0.8637 (tm-30) cc_final: 0.7937 (tm-30) REVERT: A 287 TRP cc_start: 0.9098 (t60) cc_final: 0.8888 (t60) REVERT: A 331 ASN cc_start: 0.8490 (t0) cc_final: 0.8088 (t0) REVERT: A 333 MET cc_start: 0.8617 (mmp) cc_final: 0.8411 (mmm) REVERT: A 348 ARG cc_start: 0.8575 (ttp-170) cc_final: 0.7803 (ttp-170) REVERT: A 356 SER cc_start: 0.9012 (OUTLIER) cc_final: 0.8673 (p) REVERT: A 376 MET cc_start: 0.8501 (tmm) cc_final: 0.8083 (tmm) REVERT: A 390 ILE cc_start: 0.9042 (mm) cc_final: 0.8805 (pt) REVERT: A 397 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8620 (mp10) REVERT: A 474 LYS cc_start: 0.9026 (mtmt) cc_final: 0.8563 (mmtt) REVERT: B 12 LYS cc_start: 0.7800 (ttpp) cc_final: 0.7247 (tmmt) REVERT: B 16 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9173 (mp0) REVERT: B 93 TRP cc_start: 0.6507 (OUTLIER) cc_final: 0.5747 (t60) outliers start: 34 outliers final: 22 residues processed: 138 average time/residue: 0.1640 time to fit residues: 28.8210 Evaluate side-chains 122 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 41 LYS Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 73 LEU 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 25 optimal weight: 0.4980 chunk 57 optimal weight: 0.2980 chunk 26 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 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 = 0.3608 r_free = 0.3608 target = 0.087030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.065215 restraints weight = 15862.585| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 5.05 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5050 Z= 0.118 Angle : 0.615 10.734 6866 Z= 0.305 Chirality : 0.042 0.146 763 Planarity : 0.004 0.047 838 Dihedral : 7.768 59.676 715 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.66 % Favored : 98.17 % Rotamer: Outliers : 6.24 % Allowed : 22.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.35), residues: 601 helix: 1.57 (0.29), residues: 321 sheet: 0.59 (0.50), residues: 109 loop : -0.76 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 93 HIS 0.003 0.001 HIS A 195 PHE 0.014 0.001 PHE A 49 TYR 0.018 0.001 TYR A 414 ARG 0.007 0.001 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 277) hydrogen bonds : angle 4.50112 ( 810) SS BOND : bond 0.00149 ( 2) SS BOND : angle 1.39505 ( 4) covalent geometry : bond 0.00259 ( 5048) covalent geometry : angle 0.61471 ( 6862) *********************** 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 137 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8979 (tp) REVERT: A 178 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6974 (mtp85) REVERT: A 191 ASP cc_start: 0.9181 (t0) cc_final: 0.8813 (t0) REVERT: A 230 GLU cc_start: 0.8631 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 281 ASN cc_start: 0.9457 (OUTLIER) cc_final: 0.9226 (p0) REVERT: A 282 GLU cc_start: 0.9418 (tp30) cc_final: 0.8728 (tt0) REVERT: A 333 MET cc_start: 0.8654 (mmp) cc_final: 0.7699 (mmm) REVERT: A 356 SER cc_start: 0.8950 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 376 MET cc_start: 0.8507 (tmm) cc_final: 0.8273 (tmm) REVERT: A 390 ILE cc_start: 0.9083 (mm) cc_final: 0.8828 (pt) REVERT: A 476 PHE cc_start: 0.8881 (m-10) cc_final: 0.8547 (m-10) REVERT: B 12 LYS cc_start: 0.7820 (ttpp) cc_final: 0.7264 (tmmt) REVERT: B 16 GLU cc_start: 0.9376 (mt-10) cc_final: 0.8975 (mp0) REVERT: B 45 LYS cc_start: 0.9439 (tppt) cc_final: 0.9237 (tptp) outliers start: 33 outliers final: 19 residues processed: 130 average time/residue: 0.1630 time to fit residues: 27.6982 Evaluate side-chains 113 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 281 ASN 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 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 54 ARG Chi-restraints excluded: chain B residue 87 THR 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 52 optimal weight: 0.0070 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.0060 chunk 12 optimal weight: 6.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3604 r_free = 0.3604 target = 0.086810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.065216 restraints weight = 15859.064| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 5.04 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5050 Z= 0.112 Angle : 0.579 8.854 6866 Z= 0.289 Chirality : 0.042 0.192 763 Planarity : 0.004 0.049 838 Dihedral : 7.460 58.522 708 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.66 % Favored : 98.17 % Rotamer: Outliers : 6.24 % Allowed : 22.68 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.34), residues: 601 helix: 1.70 (0.29), residues: 321 sheet: 0.58 (0.50), residues: 109 loop : -0.57 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 93 HIS 0.002 0.000 HIS A 195 PHE 0.013 0.001 PHE A 49 TYR 0.017 0.001 TYR A 373 ARG 0.005 0.001 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 277) hydrogen bonds : angle 4.38692 ( 810) SS BOND : bond 0.00181 ( 2) SS BOND : angle 1.27422 ( 4) covalent geometry : bond 0.00248 ( 5048) covalent geometry : angle 0.57843 ( 6862) *********************** 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 133 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: A 88 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8965 (tp) REVERT: A 178 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7491 (mtp85) REVERT: A 190 MET cc_start: 0.8616 (mtp) cc_final: 0.8348 (mtp) REVERT: A 191 ASP cc_start: 0.9296 (t0) cc_final: 0.8864 (t0) REVERT: A 230 GLU cc_start: 0.8647 (tm-30) cc_final: 0.7955 (tm-30) REVERT: A 266 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: A 282 GLU cc_start: 0.9419 (tp30) cc_final: 0.8771 (tt0) REVERT: A 333 MET cc_start: 0.8395 (mmp) cc_final: 0.7940 (mmm) REVERT: A 356 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8600 (p) REVERT: A 376 MET cc_start: 0.8521 (tmm) cc_final: 0.8231 (tmm) REVERT: A 390 ILE cc_start: 0.9093 (mm) cc_final: 0.8827 (pt) REVERT: B 12 LYS cc_start: 0.7841 (ttpp) cc_final: 0.7459 (tmmt) REVERT: B 16 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8696 (mp0) REVERT: B 54 ARG cc_start: 0.7923 (mtp180) cc_final: 0.6832 (mtp-110) REVERT: B 93 TRP cc_start: 0.6488 (OUTLIER) cc_final: 0.5675 (t60) outliers start: 33 outliers final: 19 residues processed: 127 average time/residue: 0.2246 time to fit residues: 37.6286 Evaluate side-chains 111 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 66 MET 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 266 GLN Chi-restraints excluded: chain A residue 272 LEU 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 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 8 THR Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 93 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 40.0000 chunk 47 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 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 = 0.3582 r_free = 0.3582 target = 0.085572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063729 restraints weight = 15837.803| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.98 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5050 Z= 0.119 Angle : 0.589 9.299 6866 Z= 0.293 Chirality : 0.042 0.214 763 Planarity : 0.005 0.071 838 Dihedral : 7.297 58.926 708 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.16 % Favored : 97.67 % Rotamer: Outliers : 6.99 % Allowed : 21.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.35), residues: 601 helix: 1.77 (0.29), residues: 321 sheet: 0.54 (0.51), residues: 109 loop : -0.46 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.002 0.001 HIS B 82 PHE 0.012 0.001 PHE A 49 TYR 0.015 0.001 TYR A 414 ARG 0.011 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 277) hydrogen bonds : angle 4.32472 ( 810) SS BOND : bond 0.00229 ( 2) SS BOND : angle 1.04207 ( 4) covalent geometry : bond 0.00268 ( 5048) covalent geometry : angle 0.58887 ( 6862) *********************** 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 134 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7638 (mtp85) REVERT: A 191 ASP cc_start: 0.9352 (t0) cc_final: 0.8972 (t0) REVERT: A 230 GLU cc_start: 0.8703 (tm-30) cc_final: 0.7998 (tm-30) REVERT: A 236 THR cc_start: 0.9117 (p) cc_final: 0.8772 (t) REVERT: A 266 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: A 278 ASP cc_start: 0.9502 (t0) cc_final: 0.9089 (m-30) REVERT: A 282 GLU cc_start: 0.9409 (tp30) cc_final: 0.8685 (tm-30) REVERT: A 348 ARG cc_start: 0.8543 (ttp-170) cc_final: 0.8234 (ttp-170) REVERT: A 376 MET cc_start: 0.8548 (tmm) cc_final: 0.8222 (tmm) REVERT: A 390 ILE cc_start: 0.9138 (mm) cc_final: 0.8853 (pt) REVERT: A 438 MET cc_start: 0.9136 (mmm) cc_final: 0.8926 (mmm) REVERT: B 12 LYS cc_start: 0.7790 (ttpp) cc_final: 0.7455 (tmmt) REVERT: B 16 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8679 (mp0) REVERT: B 93 TRP cc_start: 0.6580 (OUTLIER) cc_final: 0.5729 (t60) REVERT: B 95 ILE cc_start: 0.8655 (mm) cc_final: 0.7987 (mm) outliers start: 37 outliers final: 22 residues processed: 128 average time/residue: 0.2162 time to fit residues: 37.2452 Evaluate side-chains 116 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 66 MET 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 336 ILE 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 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 8 THR Chi-restraints excluded: chain B residue 22 CYS 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 48 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 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 = 0.3455 r_free = 0.3455 target = 0.079379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.056815 restraints weight = 16206.535| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 4.81 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5050 Z= 0.239 Angle : 0.656 7.514 6866 Z= 0.341 Chirality : 0.045 0.228 763 Planarity : 0.005 0.052 838 Dihedral : 7.332 59.512 708 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.50 % Favored : 97.34 % Rotamer: Outliers : 6.81 % Allowed : 21.17 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.35), residues: 601 helix: 1.72 (0.30), residues: 318 sheet: 0.46 (0.51), residues: 111 loop : -0.51 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 93 HIS 0.007 0.002 HIS B 82 PHE 0.014 0.002 PHE A 252 TYR 0.020 0.002 TYR A 373 ARG 0.006 0.001 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 277) hydrogen bonds : angle 4.54791 ( 810) SS BOND : bond 0.00363 ( 2) SS BOND : angle 0.97836 ( 4) covalent geometry : bond 0.00530 ( 5048) covalent geometry : angle 0.65616 ( 6862) *********************** 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 123 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7142 (mtp85) REVERT: A 191 ASP cc_start: 0.9456 (t0) cc_final: 0.9099 (t0) REVERT: A 230 GLU cc_start: 0.8698 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 266 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: A 278 ASP cc_start: 0.9508 (t0) cc_final: 0.9055 (m-30) REVERT: A 279 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.8984 (tt) REVERT: A 282 GLU cc_start: 0.9436 (tp30) cc_final: 0.8887 (tm-30) REVERT: A 390 ILE cc_start: 0.9255 (mm) cc_final: 0.9019 (tt) REVERT: B 12 LYS cc_start: 0.7872 (ttpp) cc_final: 0.7496 (tmmt) REVERT: B 16 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8673 (mp0) outliers start: 36 outliers final: 28 residues processed: 117 average time/residue: 0.1601 time to fit residues: 24.4552 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 : 0.536 ------------------------------------------------------------------------------- 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 190 MET 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 279 ILE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 336 ILE 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 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 A residue 533 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 73 LEU 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: 0.2980 chunk 22 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.082193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060068 restraints weight = 15891.987| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.84 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5050 Z= 0.120 Angle : 0.631 11.095 6866 Z= 0.311 Chirality : 0.043 0.195 763 Planarity : 0.004 0.052 838 Dihedral : 7.279 59.866 708 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.66 % Favored : 98.17 % Rotamer: Outliers : 6.05 % Allowed : 22.12 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.35), residues: 601 helix: 1.74 (0.29), residues: 318 sheet: 0.60 (0.52), residues: 107 loop : -0.56 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 93 HIS 0.008 0.001 HIS B 82 PHE 0.021 0.001 PHE A 476 TYR 0.021 0.001 TYR A 373 ARG 0.004 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 277) hydrogen bonds : angle 4.36621 ( 810) SS BOND : bond 0.00266 ( 2) SS BOND : angle 0.75549 ( 4) covalent geometry : bond 0.00268 ( 5048) covalent geometry : angle 0.63139 ( 6862) *********************** 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 124 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7020 (mtp85) REVERT: A 191 ASP cc_start: 0.9449 (t0) cc_final: 0.9144 (t0) REVERT: A 230 GLU cc_start: 0.8584 (tm-30) cc_final: 0.7961 (tm-30) REVERT: A 266 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: A 278 ASP cc_start: 0.9464 (t0) cc_final: 0.9076 (m-30) REVERT: A 279 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9014 (tt) REVERT: A 282 GLU cc_start: 0.9421 (tp30) cc_final: 0.8874 (tm-30) REVERT: A 348 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.8290 (ttp-170) REVERT: A 376 MET cc_start: 0.8691 (tpp) cc_final: 0.8412 (tmm) REVERT: A 438 MET cc_start: 0.9086 (mmm) cc_final: 0.8856 (mmm) REVERT: B 12 LYS cc_start: 0.7860 (ttpp) cc_final: 0.7513 (tmmt) REVERT: B 16 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8723 (mp0) REVERT: B 74 ARG cc_start: 0.9502 (ptp90) cc_final: 0.9265 (ptp90) REVERT: B 86 TYR cc_start: 0.8960 (m-80) cc_final: 0.8517 (m-80) REVERT: B 87 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8391 (p) REVERT: B 93 TRP cc_start: 0.6724 (OUTLIER) cc_final: 0.6202 (t60) outliers start: 32 outliers final: 20 residues processed: 121 average time/residue: 0.1755 time to fit residues: 27.7013 Evaluate side-chains 104 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 190 MET 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 279 ILE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 336 ILE 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 403 VAL 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 22 CYS 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 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3458 r_free = 0.3458 target = 0.079570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.057212 restraints weight = 16074.920| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 4.79 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4840 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= 0.181 Angle : 0.645 8.718 6866 Z= 0.329 Chirality : 0.044 0.186 763 Planarity : 0.004 0.051 838 Dihedral : 6.998 57.509 707 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.50 % Favored : 97.34 % Rotamer: Outliers : 6.05 % Allowed : 23.06 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.35), residues: 601 helix: 1.75 (0.29), residues: 317 sheet: 0.33 (0.51), residues: 111 loop : -0.51 (0.47), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 93 HIS 0.007 0.001 HIS B 82 PHE 0.014 0.002 PHE A 476 TYR 0.020 0.002 TYR A 373 ARG 0.005 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 277) hydrogen bonds : angle 4.38878 ( 810) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.46161 ( 4) covalent geometry : bond 0.00408 ( 5048) covalent geometry : angle 0.64545 ( 6862) *********************** 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 119 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7770 (mtp85) REVERT: A 191 ASP cc_start: 0.9476 (t0) cc_final: 0.9153 (t0) REVERT: A 230 GLU cc_start: 0.8587 (tm-30) cc_final: 0.7925 (tm-30) REVERT: A 266 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: A 278 ASP cc_start: 0.9456 (t0) cc_final: 0.9027 (m-30) REVERT: A 279 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9127 (tt) REVERT: A 282 GLU cc_start: 0.9436 (tp30) cc_final: 0.8929 (tm-30) REVERT: A 348 ARG cc_start: 0.8622 (ttp-170) cc_final: 0.8343 (ttp-170) REVERT: A 390 ILE cc_start: 0.8624 (tt) cc_final: 0.8204 (pt) REVERT: B 12 LYS cc_start: 0.7886 (ttpp) cc_final: 0.7413 (ttpt) REVERT: B 16 GLU cc_start: 0.9241 (mt-10) cc_final: 0.9004 (mt-10) REVERT: B 26 ASP cc_start: 0.9048 (m-30) cc_final: 0.8836 (t0) REVERT: B 86 TYR cc_start: 0.8977 (m-80) cc_final: 0.8732 (m-80) REVERT: B 87 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8420 (p) REVERT: B 93 TRP cc_start: 0.6898 (OUTLIER) cc_final: 0.6344 (t60) REVERT: B 95 ILE cc_start: 0.9014 (mm) cc_final: 0.8340 (mm) outliers start: 32 outliers final: 23 residues processed: 113 average time/residue: 0.1732 time to fit residues: 25.3653 Evaluate side-chains 110 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 190 MET 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 279 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 336 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 479 THR 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 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 20 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3499 r_free = 0.3499 target = 0.081379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.059748 restraints weight = 15678.278| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.71 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4896 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= 0.122 Angle : 0.650 9.270 6866 Z= 0.321 Chirality : 0.043 0.177 763 Planarity : 0.004 0.054 838 Dihedral : 6.964 58.881 707 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.66 % Favored : 98.17 % Rotamer: Outliers : 5.86 % Allowed : 23.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.34), residues: 601 helix: 1.72 (0.29), residues: 318 sheet: 0.60 (0.52), residues: 107 loop : -0.55 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 93 HIS 0.007 0.001 HIS B 82 PHE 0.012 0.001 PHE B 38 TYR 0.021 0.001 TYR A 373 ARG 0.005 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 277) hydrogen bonds : angle 4.27446 ( 810) SS BOND : bond 0.00210 ( 2) SS BOND : angle 0.52538 ( 4) covalent geometry : bond 0.00273 ( 5048) covalent geometry : angle 0.64970 ( 6862) *********************** 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 116 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7123 (mtp85) REVERT: A 191 ASP cc_start: 0.9451 (t0) cc_final: 0.9149 (t0) REVERT: A 230 GLU cc_start: 0.8536 (tm-30) cc_final: 0.7946 (tm-30) REVERT: A 266 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: A 278 ASP cc_start: 0.9428 (t0) cc_final: 0.9003 (m-30) REVERT: A 279 ILE cc_start: 0.9494 (OUTLIER) cc_final: 0.9126 (tt) REVERT: A 282 GLU cc_start: 0.9428 (tp30) cc_final: 0.8913 (tm-30) REVERT: A 348 ARG cc_start: 0.8613 (ttp-170) cc_final: 0.8382 (ttp-170) REVERT: A 390 ILE cc_start: 0.8583 (tt) cc_final: 0.8164 (pt) REVERT: B 12 LYS cc_start: 0.7835 (ttpp) cc_final: 0.7164 (tmmt) REVERT: B 16 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8826 (mt-10) REVERT: B 18 LEU cc_start: 0.9452 (tt) cc_final: 0.9008 (mm) REVERT: B 26 ASP cc_start: 0.9077 (m-30) cc_final: 0.8846 (t0) REVERT: B 87 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 93 TRP cc_start: 0.6792 (OUTLIER) cc_final: 0.6190 (t60) REVERT: B 95 ILE cc_start: 0.9040 (mm) cc_final: 0.8357 (mm) outliers start: 31 outliers final: 24 residues processed: 109 average time/residue: 0.1786 time to fit residues: 25.2919 Evaluate side-chains 110 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 141 ASN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 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 279 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 350 ILE 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 479 THR 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 20 ILE Chi-restraints excluded: chain B residue 22 CYS 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 17 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 0.0980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3493 r_free = 0.3493 target = 0.081699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.059789 restraints weight = 15838.880| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 4.84 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5005 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= 0.121 Angle : 0.649 9.337 6866 Z= 0.320 Chirality : 0.044 0.176 763 Planarity : 0.004 0.055 838 Dihedral : 6.800 57.976 707 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.00 % Favored : 97.84 % Rotamer: Outliers : 5.67 % Allowed : 23.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.34), residues: 601 helix: 1.70 (0.29), residues: 318 sheet: 0.54 (0.51), residues: 107 loop : -0.54 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 93 HIS 0.006 0.001 HIS B 82 PHE 0.012 0.001 PHE B 38 TYR 0.021 0.001 TYR A 373 ARG 0.006 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 277) hydrogen bonds : angle 4.24179 ( 810) SS BOND : bond 0.00222 ( 2) SS BOND : angle 0.46432 ( 4) covalent geometry : bond 0.00272 ( 5048) covalent geometry : angle 0.64955 ( 6862) ********************** 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 114 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7803 (mtp85) REVERT: A 191 ASP cc_start: 0.9433 (t0) cc_final: 0.9143 (t0) REVERT: A 230 GLU cc_start: 0.8557 (tm-30) cc_final: 0.7956 (tm-30) REVERT: A 266 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: A 278 ASP cc_start: 0.9396 (t0) cc_final: 0.8993 (m-30) REVERT: A 279 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9163 (tt) REVERT: A 282 GLU cc_start: 0.9428 (tp30) cc_final: 0.8890 (tm-30) REVERT: A 390 ILE cc_start: 0.8572 (tt) cc_final: 0.8154 (pt) REVERT: A 471 LEU cc_start: 0.9649 (pp) cc_final: 0.9339 (tt) REVERT: B 12 LYS cc_start: 0.7785 (ttpp) cc_final: 0.7408 (tttt) REVERT: B 16 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8776 (mt-10) REVERT: B 93 TRP cc_start: 0.6753 (OUTLIER) cc_final: 0.5938 (t60) REVERT: B 95 ILE cc_start: 0.9095 (mm) cc_final: 0.8455 (mm) outliers start: 30 outliers final: 25 residues processed: 107 average time/residue: 0.1663 time to fit residues: 22.8517 Evaluate side-chains 111 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 141 ASN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 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 279 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 350 ILE 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 479 THR 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 8 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 22 CYS 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 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN ** 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 = 0.3492 r_free = 0.3492 target = 0.081668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.059676 restraints weight = 15886.482| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.81 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5123 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= 0.122 Angle : 0.643 9.423 6866 Z= 0.319 Chirality : 0.044 0.171 763 Planarity : 0.004 0.055 838 Dihedral : 6.679 57.890 707 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.83 % Favored : 98.00 % Rotamer: Outliers : 5.29 % Allowed : 23.82 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.34), residues: 601 helix: 1.71 (0.29), residues: 318 sheet: 0.55 (0.51), residues: 107 loop : -0.57 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.006 0.001 HIS B 82 PHE 0.011 0.001 PHE B 38 TYR 0.021 0.001 TYR A 373 ARG 0.004 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 277) hydrogen bonds : angle 4.16693 ( 810) SS BOND : bond 0.00226 ( 2) SS BOND : angle 0.55630 ( 4) covalent geometry : bond 0.00272 ( 5048) covalent geometry : angle 0.64306 ( 6862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2990.29 seconds wall clock time: 52 minutes 53.69 seconds (3173.69 seconds total)