Starting phenix.real_space_refine on Tue Jun 10 03:57:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qpa_14116/06_2025/7qpa_14116_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qpa_14116/06_2025/7qpa_14116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qpa_14116/06_2025/7qpa_14116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qpa_14116/06_2025/7qpa_14116.map" model { file = "/net/cci-nas-00/data/ceres_data/7qpa_14116/06_2025/7qpa_14116_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qpa_14116/06_2025/7qpa_14116_trim.cif" } resolution = 3.18 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 34 5.16 5 C 3508 2.51 5 N 804 2.21 5 O 926 1.98 5 H 5540 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 10814 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5244 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "B" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5244 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "A" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'DLP': 2, 'IAC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 87 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 105 Classifications: {'water': 35} Link IDs: {None: 34} Time building chain proxies: 5.77, per 1000 atoms: 0.53 Number of scatterers: 10814 At special positions: 0 Unit cell: (76.346, 100.932, 67.288, 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) S 34 16.00 P 2 15.00 O 926 8.00 N 804 7.00 C 3508 6.00 H 5540 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 716.5 milliseconds 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 87.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 3 through 30 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 51 through 61 removed outlier: 3.866A pdb=" N GLN A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 93 removed outlier: 3.534A pdb=" N PHE A 92 " --> pdb=" O MET A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.726A pdb=" N ARG A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.676A pdb=" N ALA A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.938A pdb=" N ALA A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 207 through 220 removed outlier: 3.674A pdb=" N LEU A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.906A pdb=" N TYR A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.915A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 274 Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.777A pdb=" N ILE A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 339 through 351 removed outlier: 4.108A pdb=" N ILE A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 367 removed outlier: 4.043A pdb=" N LEU A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 29 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 51 through 61 removed outlier: 3.846A pdb=" N GLN B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.781A pdb=" N MET B 67 " --> pdb=" O PRO B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 93 removed outlier: 3.686A pdb=" N PHE B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.536A pdb=" N ALA B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 148 removed outlier: 4.046A pdb=" N SER B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 163 Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.688A pdb=" N LEU B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.660A pdb=" N TYR B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.945A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 274 Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 311 through 320 removed outlier: 3.687A pdb=" N ILE B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.798A pdb=" N THR B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 367 removed outlier: 4.070A pdb=" N LEU B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1134 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: 4.00 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5534 1.03 - 1.23: 13 1.23 - 1.42: 2091 1.42 - 1.62: 3172 1.62 - 1.81: 62 Bond restraints: 10872 Sorted by residual: bond pdb=" N IAC A 401 " pdb=" C8 IAC A 401 " ideal model delta sigma weight residual 1.371 1.315 0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" N IAC B 401 " pdb=" C8 IAC B 401 " ideal model delta sigma weight residual 1.371 1.315 0.056 2.00e-02 2.50e+03 7.76e+00 bond pdb=" O4P DLP A 402 " pdb=" P DLP A 402 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" O4P DLP A 403 " pdb=" P DLP A 403 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C4 DLP A 403 " pdb=" O4P DLP A 403 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.11e+00 ... (remaining 10867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 19377 2.09 - 4.18: 183 4.18 - 6.27: 10 6.27 - 8.36: 4 8.36 - 10.45: 2 Bond angle restraints: 19576 Sorted by residual: angle pdb=" O3P DLP A 403 " pdb=" P DLP A 403 " pdb=" O4P DLP A 403 " ideal model delta sigma weight residual 93.58 104.03 -10.45 3.00e+00 1.11e-01 1.21e+01 angle pdb=" O3P DLP A 402 " pdb=" P DLP A 402 " pdb=" O4P DLP A 402 " ideal model delta sigma weight residual 93.58 103.82 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N VAL A 106 " pdb=" CA VAL A 106 " pdb=" C VAL A 106 " ideal model delta sigma weight residual 113.00 109.51 3.49 1.30e+00 5.92e-01 7.20e+00 angle pdb=" N ILE B 318 " pdb=" CA ILE B 318 " pdb=" C ILE B 318 " ideal model delta sigma weight residual 112.96 110.36 2.60 1.00e+00 1.00e+00 6.78e+00 angle pdb=" C18 IAC A 401 " pdb=" C17 IAC A 401 " pdb=" C7 IAC A 401 " ideal model delta sigma weight residual 115.88 109.02 6.86 3.00e+00 1.11e-01 5.23e+00 ... (remaining 19571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.15: 4688 23.15 - 46.30: 260 46.30 - 69.45: 70 69.45 - 92.60: 8 92.60 - 115.75: 2 Dihedral angle restraints: 5028 sinusoidal: 2762 harmonic: 2266 Sorted by residual: dihedral pdb=" N DLP A 403 " pdb=" C4 DLP A 403 " pdb=" C5 DLP A 403 " pdb=" O4P DLP A 403 " ideal model delta sinusoidal sigma weight residual 288.95 173.20 115.75 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" N DLP A 402 " pdb=" C4 DLP A 402 " pdb=" C5 DLP A 402 " pdb=" O4P DLP A 402 " ideal model delta sinusoidal sigma weight residual 288.95 174.87 114.08 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" CA SER B 113 " pdb=" C SER B 113 " pdb=" N VAL B 114 " pdb=" CA VAL B 114 " ideal model delta harmonic sigma weight residual 180.00 -162.86 -17.14 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 637 0.040 - 0.079: 189 0.079 - 0.119: 30 0.119 - 0.159: 3 0.159 - 0.199: 3 Chirality restraints: 862 Sorted by residual: chirality pdb=" C2 DLP A 403 " pdb=" C1 DLP A 403 " pdb=" C3 DLP A 403 " pdb=" O2 DLP A 403 " both_signs ideal model delta sigma weight residual False -2.35 -2.55 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" C2 DLP A 402 " pdb=" C1 DLP A 402 " pdb=" C3 DLP A 402 " pdb=" O2 DLP A 402 " both_signs ideal model delta sigma weight residual False -2.35 -2.55 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CG LEU B 5 " pdb=" CB LEU B 5 " pdb=" CD1 LEU B 5 " pdb=" CD2 LEU B 5 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 859 not shown) Planarity restraints: 1472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 68 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO B 69 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 69 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 69 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 328 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 329 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 216 " 0.136 9.50e-02 1.11e+02 4.56e-02 2.57e+00 pdb=" NE ARG A 216 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 216 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 216 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 216 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 216 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 216 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 216 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 216 " 0.000 2.00e-02 2.50e+03 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 62 2.04 - 2.68: 16669 2.68 - 3.32: 33261 3.32 - 3.96: 42515 3.96 - 4.60: 66955 Nonbonded interactions: 159462 Sorted by model distance: nonbonded pdb="HD21 LEU B 5 " pdb=" HE1 HIS B 9 " model vdw 1.404 2.270 nonbonded pdb="HD21 ASN A 117 " pdb=" O HOH A 501 " model vdw 1.644 2.450 nonbonded pdb="HD21 ASN B 117 " pdb=" O HOH B 501 " model vdw 1.647 2.450 nonbonded pdb=" OD1 ASN A 63 " pdb=" H PHE A 65 " model vdw 1.667 2.450 nonbonded pdb=" HZ3 LYS B 334 " pdb=" O HOH B 503 " model vdw 1.707 2.450 ... (remaining 159457 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 0 through 367 or resid 401)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.310 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 0.004 0.056 5332 Z= 0.204 Angle : 0.638 10.454 7224 Z= 0.310 Chirality : 0.038 0.199 862 Planarity : 0.005 0.060 854 Dihedral : 15.169 115.750 1936 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 1.43 (0.33), residues: 646 helix: 1.66 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.71 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 93 HIS 0.010 0.001 HIS A 94 PHE 0.015 0.001 PHE A 330 TYR 0.007 0.001 TYR B 8 ARG 0.010 0.001 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.12476 ( 379) hydrogen bonds : angle 6.73809 ( 1134) covalent geometry : bond 0.00438 ( 5332) covalent geometry : angle 0.63780 ( 7224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.772 Fit side-chains REVERT: A 67 MET cc_start: 0.8540 (mtm) cc_final: 0.8321 (mtp) REVERT: A 308 ARG cc_start: 0.7457 (mmt-90) cc_final: 0.7256 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.3453 time to fit residues: 42.2493 Evaluate side-chains 83 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.167038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137586 restraints weight = 16637.867| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.78 r_work: 0.3358 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5332 Z= 0.164 Angle : 0.566 5.190 7224 Z= 0.293 Chirality : 0.037 0.128 862 Planarity : 0.005 0.046 854 Dihedral : 11.614 104.762 772 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.72 % Allowed : 5.60 % Favored : 93.68 % 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: 1.04 (0.33), residues: 646 helix: 1.35 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.08 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.009 0.001 HIS A 94 PHE 0.016 0.001 PHE A 330 TYR 0.007 0.001 TYR B 8 ARG 0.004 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 379) hydrogen bonds : angle 5.45567 ( 1134) covalent geometry : bond 0.00368 ( 5332) covalent geometry : angle 0.56594 ( 7224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.732 Fit side-chains REVERT: A 67 MET cc_start: 0.8655 (mtm) cc_final: 0.8430 (mtp) REVERT: A 208 MET cc_start: 0.6811 (tpp) cc_final: 0.6424 (tpt) REVERT: A 308 ARG cc_start: 0.7071 (mmt-90) cc_final: 0.6156 (mtm180) REVERT: B 308 ARG cc_start: 0.7461 (mmt-90) cc_final: 0.7122 (mmt-90) outliers start: 4 outliers final: 3 residues processed: 85 average time/residue: 0.3590 time to fit residues: 40.3087 Evaluate side-chains 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.165681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.135912 restraints weight = 16886.967| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.79 r_work: 0.3344 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5332 Z= 0.164 Angle : 0.550 5.025 7224 Z= 0.284 Chirality : 0.037 0.128 862 Planarity : 0.005 0.047 854 Dihedral : 11.517 99.157 772 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.54 % Allowed : 7.40 % Favored : 92.06 % 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: 0.88 (0.33), residues: 646 helix: 1.26 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.26 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 233 HIS 0.006 0.001 HIS A 94 PHE 0.016 0.001 PHE A 330 TYR 0.007 0.001 TYR B 361 ARG 0.005 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 379) hydrogen bonds : angle 5.26143 ( 1134) covalent geometry : bond 0.00383 ( 5332) covalent geometry : angle 0.54962 ( 7224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.720 Fit side-chains REVERT: A 208 MET cc_start: 0.6794 (tpp) cc_final: 0.6430 (tpt) REVERT: A 308 ARG cc_start: 0.6995 (mmt-90) cc_final: 0.6099 (mtm180) REVERT: B 308 ARG cc_start: 0.7342 (mmt-90) cc_final: 0.7027 (mmt-90) outliers start: 3 outliers final: 3 residues processed: 78 average time/residue: 0.3550 time to fit residues: 36.5694 Evaluate side-chains 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 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 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.166098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.136552 restraints weight = 16789.602| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.78 r_work: 0.3342 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5332 Z= 0.142 Angle : 0.529 5.063 7224 Z= 0.273 Chirality : 0.036 0.125 862 Planarity : 0.005 0.047 854 Dihedral : 11.439 94.192 772 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.72 % Allowed : 7.94 % Favored : 91.34 % 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: 0.98 (0.33), residues: 646 helix: 1.35 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.33 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 233 HIS 0.006 0.001 HIS A 94 PHE 0.015 0.001 PHE A 330 TYR 0.006 0.001 TYR B 361 ARG 0.006 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 379) hydrogen bonds : angle 5.09927 ( 1134) covalent geometry : bond 0.00326 ( 5332) covalent geometry : angle 0.52892 ( 7224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.838 Fit side-chains REVERT: A 208 MET cc_start: 0.6780 (tpp) cc_final: 0.6434 (tpt) REVERT: A 308 ARG cc_start: 0.7013 (mmt-90) cc_final: 0.6106 (mtm180) outliers start: 4 outliers final: 4 residues processed: 81 average time/residue: 0.3789 time to fit residues: 40.6870 Evaluate side-chains 80 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 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 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.165806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134883 restraints weight = 16776.339| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.90 r_work: 0.3317 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5332 Z= 0.141 Angle : 0.523 4.968 7224 Z= 0.270 Chirality : 0.036 0.132 862 Planarity : 0.005 0.046 854 Dihedral : 11.490 88.667 772 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.90 % Allowed : 8.66 % Favored : 90.43 % 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: 1.03 (0.33), residues: 646 helix: 1.39 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.35 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.004 0.001 HIS B 237 PHE 0.015 0.001 PHE A 330 TYR 0.006 0.001 TYR B 361 ARG 0.003 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 379) hydrogen bonds : angle 5.01251 ( 1134) covalent geometry : bond 0.00329 ( 5332) covalent geometry : angle 0.52293 ( 7224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.758 Fit side-chains REVERT: A 208 MET cc_start: 0.6721 (tpp) cc_final: 0.6391 (tpt) REVERT: A 308 ARG cc_start: 0.6992 (mmt-90) cc_final: 0.6064 (mtm180) outliers start: 5 outliers final: 3 residues processed: 81 average time/residue: 0.3897 time to fit residues: 42.1680 Evaluate side-chains 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 48 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.166098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136299 restraints weight = 16819.263| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.79 r_work: 0.3333 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5332 Z= 0.146 Angle : 0.528 4.895 7224 Z= 0.273 Chirality : 0.037 0.155 862 Planarity : 0.005 0.046 854 Dihedral : 11.485 84.570 772 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.90 % Allowed : 8.66 % Favored : 90.43 % 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: 1.00 (0.33), residues: 646 helix: 1.37 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.36 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.011 0.001 HIS A 94 PHE 0.015 0.001 PHE A 330 TYR 0.006 0.001 TYR B 361 ARG 0.004 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 379) hydrogen bonds : angle 4.98055 ( 1134) covalent geometry : bond 0.00338 ( 5332) covalent geometry : angle 0.52763 ( 7224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.672 Fit side-chains REVERT: A 208 MET cc_start: 0.6783 (tpp) cc_final: 0.6453 (tpt) REVERT: A 308 ARG cc_start: 0.7044 (mmt-90) cc_final: 0.6120 (mtm180) outliers start: 5 outliers final: 5 residues processed: 75 average time/residue: 0.4024 time to fit residues: 39.9284 Evaluate side-chains 76 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 54 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.165500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.134307 restraints weight = 16921.469| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.92 r_work: 0.3309 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5332 Z= 0.150 Angle : 0.529 4.964 7224 Z= 0.273 Chirality : 0.037 0.126 862 Planarity : 0.005 0.045 854 Dihedral : 11.409 87.339 772 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.72 % Allowed : 9.39 % Favored : 89.89 % 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: 0.94 (0.33), residues: 646 helix: 1.28 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -2.29 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.008 0.001 HIS A 94 PHE 0.015 0.001 PHE A 330 TYR 0.007 0.001 TYR A 361 ARG 0.002 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 379) hydrogen bonds : angle 4.93652 ( 1134) covalent geometry : bond 0.00352 ( 5332) covalent geometry : angle 0.52915 ( 7224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.837 Fit side-chains REVERT: A 208 MET cc_start: 0.6711 (tpp) cc_final: 0.6390 (tpt) REVERT: A 286 ILE cc_start: 0.8166 (tp) cc_final: 0.7441 (pt) REVERT: A 308 ARG cc_start: 0.7012 (mmt-90) cc_final: 0.6075 (mtm180) outliers start: 4 outliers final: 4 residues processed: 75 average time/residue: 0.4449 time to fit residues: 44.0497 Evaluate side-chains 74 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 24 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.167127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.137461 restraints weight = 16687.497| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.79 r_work: 0.3345 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5332 Z= 0.126 Angle : 0.508 4.756 7224 Z= 0.262 Chirality : 0.036 0.126 862 Planarity : 0.005 0.045 854 Dihedral : 11.117 86.431 772 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.26 % Allowed : 9.75 % Favored : 88.99 % 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: 1.10 (0.34), residues: 646 helix: 1.40 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -2.23 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.009 0.001 HIS A 94 PHE 0.014 0.001 PHE A 155 TYR 0.005 0.001 TYR B 361 ARG 0.003 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 379) hydrogen bonds : angle 4.85631 ( 1134) covalent geometry : bond 0.00289 ( 5332) covalent geometry : angle 0.50838 ( 7224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.732 Fit side-chains REVERT: A 208 MET cc_start: 0.6787 (tpp) cc_final: 0.6457 (tpt) REVERT: A 286 ILE cc_start: 0.8183 (tp) cc_final: 0.7465 (pt) REVERT: A 308 ARG cc_start: 0.7047 (mmt-90) cc_final: 0.6117 (mtm180) REVERT: B 9 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7132 (t-90) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 0.3734 time to fit residues: 37.9961 Evaluate side-chains 75 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.167923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.138214 restraints weight = 16853.458| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.79 r_work: 0.3347 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5332 Z= 0.127 Angle : 0.507 4.634 7224 Z= 0.261 Chirality : 0.036 0.174 862 Planarity : 0.005 0.043 854 Dihedral : 10.994 85.306 772 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.08 % Allowed : 10.11 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.33), residues: 646 helix: 1.41 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.46 (0.47), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 233 HIS 0.011 0.001 HIS A 94 PHE 0.013 0.001 PHE A 330 TYR 0.006 0.001 TYR B 130 ARG 0.001 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 379) hydrogen bonds : angle 4.81695 ( 1134) covalent geometry : bond 0.00292 ( 5332) covalent geometry : angle 0.50668 ( 7224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.793 Fit side-chains REVERT: A 67 MET cc_start: 0.8647 (mtm) cc_final: 0.8374 (mtp) REVERT: A 208 MET cc_start: 0.6766 (tpp) cc_final: 0.6443 (tpt) REVERT: A 286 ILE cc_start: 0.8183 (tp) cc_final: 0.7469 (pt) REVERT: A 308 ARG cc_start: 0.7053 (mmt-90) cc_final: 0.6118 (mtm180) REVERT: B 9 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7130 (t-90) REVERT: B 18 TYR cc_start: 0.8952 (m-80) cc_final: 0.8648 (m-80) outliers start: 6 outliers final: 5 residues processed: 76 average time/residue: 0.3967 time to fit residues: 39.5358 Evaluate side-chains 76 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 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 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.167193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137437 restraints weight = 16767.827| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.80 r_work: 0.3342 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5332 Z= 0.139 Angle : 0.516 4.693 7224 Z= 0.266 Chirality : 0.037 0.126 862 Planarity : 0.005 0.043 854 Dihedral : 10.891 84.885 772 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.26 % Allowed : 10.11 % Favored : 88.63 % 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: 1.04 (0.33), residues: 646 helix: 1.38 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.48 (0.47), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.010 0.001 HIS A 94 PHE 0.015 0.001 PHE A 155 TYR 0.006 0.001 TYR B 130 ARG 0.001 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 379) hydrogen bonds : angle 4.81625 ( 1134) covalent geometry : bond 0.00321 ( 5332) covalent geometry : angle 0.51606 ( 7224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.713 Fit side-chains REVERT: A 9 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7122 (t-90) REVERT: A 67 MET cc_start: 0.8681 (mtm) cc_final: 0.8423 (mtp) REVERT: A 208 MET cc_start: 0.6758 (tpp) cc_final: 0.6436 (tpt) REVERT: A 286 ILE cc_start: 0.8186 (tp) cc_final: 0.7469 (pt) REVERT: A 308 ARG cc_start: 0.7058 (mmt-90) cc_final: 0.6119 (mtm180) REVERT: B 9 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.7126 (t-90) REVERT: B 18 TYR cc_start: 0.8960 (m-80) cc_final: 0.8644 (m-80) outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 0.3811 time to fit residues: 39.6481 Evaluate side-chains 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 54 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.4980 chunk 56 optimal weight: 0.0870 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.167942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.138386 restraints weight = 16608.756| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.79 r_work: 0.3353 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5332 Z= 0.121 Angle : 0.504 4.569 7224 Z= 0.259 Chirality : 0.036 0.163 862 Planarity : 0.006 0.079 854 Dihedral : 10.394 81.504 772 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.08 % Allowed : 10.47 % Favored : 88.45 % 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: 1.18 (0.34), residues: 646 helix: 1.48 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.45 (0.47), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.013 0.001 HIS A 94 PHE 0.013 0.001 PHE A 330 TYR 0.005 0.001 TYR A 361 ARG 0.014 0.001 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 379) hydrogen bonds : angle 4.75189 ( 1134) covalent geometry : bond 0.00277 ( 5332) covalent geometry : angle 0.50412 ( 7224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6368.00 seconds wall clock time: 109 minutes 37.87 seconds (6577.87 seconds total)