Starting phenix.real_space_refine on Fri Aug 22 17:25:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9t_37381/08_2025/8w9t_37381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9t_37381/08_2025/8w9t_37381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w9t_37381/08_2025/8w9t_37381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9t_37381/08_2025/8w9t_37381.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9t_37381/08_2025/8w9t_37381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9t_37381/08_2025/8w9t_37381.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 46 5.16 5 Na 2 4.78 5 C 4324 2.51 5 N 1054 2.21 5 O 1148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6574 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3284 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 2 Chain: "B" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3284 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.69, per 1000 atoms: 0.26 Number of scatterers: 6574 At special positions: 0 Unit cell: (101.37, 84.63, 86.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 Na 2 11.00 O 1148 8.00 N 1054 7.00 C 4324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 335.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 42 through 65 removed outlier: 3.564A pdb=" N ALA A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 116 Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 179 through 216 removed outlier: 3.757A pdb=" N SER A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 229 through 244 Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 277 through 293 removed outlier: 3.648A pdb=" N ARG A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 4.060A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 342 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.216A pdb=" N ASP A 348 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 removed outlier: 3.882A pdb=" N ARG A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.528A pdb=" N LEU A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 504 through 520 removed outlier: 3.525A pdb=" N LEU A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 65 removed outlier: 3.563A pdb=" N ALA B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 Processing helix chain 'B' and resid 101 through 116 Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 179 through 216 removed outlier: 3.756A pdb=" N SER B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Proline residue: B 222 - end of helix Processing helix chain 'B' and resid 229 through 244 Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 293 removed outlier: 3.648A pdb=" N ARG B 283 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 removed outlier: 4.060A pdb=" N THR B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 342 Processing helix chain 'B' and resid 344 through 348 removed outlier: 4.216A pdb=" N ASP B 348 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 367 removed outlier: 3.882A pdb=" N ARG B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 380 through 393 removed outlier: 3.530A pdb=" N LEU B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 429 through 445 Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 479 through 485 Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 504 through 520 removed outlier: 3.526A pdb=" N LEU B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1296 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: 1.04 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1365 1.33 - 1.45: 1476 1.45 - 1.57: 3803 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6718 Sorted by residual: bond pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.25e-02 6.40e+03 4.55e+00 bond pdb=" CA ARG A 367 " pdb=" CB ARG A 367 " ideal model delta sigma weight residual 1.523 1.498 0.026 1.27e-02 6.20e+03 4.06e+00 bond pdb=" CA ARG B 367 " pdb=" CB ARG B 367 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.27e-02 6.20e+03 3.85e+00 bond pdb=" C SER B 90 " pdb=" O SER B 90 " ideal model delta sigma weight residual 1.235 1.212 0.023 1.23e-02 6.61e+03 3.47e+00 bond pdb=" CA ILE A 374 " pdb=" CB ILE A 374 " ideal model delta sigma weight residual 1.544 1.520 0.023 1.30e-02 5.92e+03 3.18e+00 ... (remaining 6713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 8806 1.34 - 2.67: 251 2.67 - 4.01: 59 4.01 - 5.35: 12 5.35 - 6.68: 6 Bond angle restraints: 9134 Sorted by residual: angle pdb=" N LEU A 87 " pdb=" CA LEU A 87 " pdb=" C LEU A 87 " ideal model delta sigma weight residual 111.28 115.08 -3.80 1.09e+00 8.42e-01 1.22e+01 angle pdb=" N LEU B 87 " pdb=" CA LEU B 87 " pdb=" C LEU B 87 " ideal model delta sigma weight residual 111.28 115.01 -3.73 1.09e+00 8.42e-01 1.17e+01 angle pdb=" N ILE A 374 " pdb=" CA ILE A 374 " pdb=" CB ILE A 374 " ideal model delta sigma weight residual 112.32 108.44 3.88 1.15e+00 7.56e-01 1.14e+01 angle pdb=" N SER B 90 " pdb=" CA SER B 90 " pdb=" C SER B 90 " ideal model delta sigma weight residual 112.04 107.41 4.63 1.44e+00 4.82e-01 1.04e+01 angle pdb=" N SER A 90 " pdb=" CA SER A 90 " pdb=" C SER A 90 " ideal model delta sigma weight residual 112.04 107.91 4.13 1.44e+00 4.82e-01 8.25e+00 ... (remaining 9129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 3572 15.72 - 31.43: 304 31.43 - 47.15: 72 47.15 - 62.87: 6 62.87 - 78.59: 4 Dihedral angle restraints: 3958 sinusoidal: 1500 harmonic: 2458 Sorted by residual: dihedral pdb=" CA ARG A 367 " pdb=" C ARG A 367 " pdb=" N HIS A 368 " pdb=" CA HIS A 368 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG B 367 " pdb=" C ARG B 367 " pdb=" N HIS B 368 " pdb=" CA HIS B 368 " ideal model delta harmonic sigma weight residual 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ASN B 365 " pdb=" C ASN B 365 " pdb=" N ALA B 366 " pdb=" CA ALA B 366 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 3955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 780 0.041 - 0.081: 264 0.081 - 0.122: 56 0.122 - 0.163: 7 0.163 - 0.203: 3 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA ILE A 374 " pdb=" N ILE A 374 " pdb=" C ILE A 374 " pdb=" CB ILE A 374 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ASN A 253 " pdb=" N ASN A 253 " pdb=" C ASN A 253 " pdb=" CB ASN A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA ASN B 253 " pdb=" N ASN B 253 " pdb=" C ASN B 253 " pdb=" CB ASN B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1107 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 88 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C THR A 88 " 0.046 2.00e-02 2.50e+03 pdb=" O THR A 88 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 89 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 252 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C GLU B 252 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU B 252 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN B 253 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 252 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.03e+00 pdb=" C GLU A 252 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU A 252 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 253 " -0.014 2.00e-02 2.50e+03 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 83 2.65 - 3.21: 6554 3.21 - 3.78: 10886 3.78 - 4.34: 15511 4.34 - 4.90: 24867 Nonbonded interactions: 57901 Sorted by model distance: nonbonded pdb=" O GLN B 424 " pdb=" OG1 THR B 527 " model vdw 2.090 3.040 nonbonded pdb=" O GLN A 424 " pdb=" OG1 THR A 527 " model vdw 2.091 3.040 nonbonded pdb=" NH2 ARG A 367 " pdb=" O PRO A 394 " model vdw 2.189 3.120 nonbonded pdb=" NH2 ARG B 367 " pdb=" O PRO B 394 " model vdw 2.189 3.120 nonbonded pdb=" O GLY B 91 " pdb=" O HOH B 801 " model vdw 2.257 3.040 ... (remaining 57896 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.620 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.060 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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 0.032 6718 Z= 0.206 Angle : 0.601 6.685 9134 Z= 0.333 Chirality : 0.043 0.203 1110 Planarity : 0.005 0.041 1108 Dihedral : 12.297 78.585 2370 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.67 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.25), residues: 840 helix: -0.90 (0.18), residues: 582 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 450 TYR 0.015 0.002 TYR B 50 PHE 0.011 0.001 PHE A 361 TRP 0.007 0.001 TRP A 287 HIS 0.007 0.002 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 6718) covalent geometry : angle 0.60119 ( 9134) hydrogen bonds : bond 0.13137 ( 448) hydrogen bonds : angle 6.20942 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.243 Fit side-chains REVERT: A 69 ASN cc_start: 0.7256 (t0) cc_final: 0.7047 (t0) REVERT: A 300 LEU cc_start: 0.7012 (mt) cc_final: 0.6743 (mm) REVERT: A 447 ARG cc_start: 0.6932 (mtp85) cc_final: 0.6616 (ttp-110) REVERT: B 300 LEU cc_start: 0.7012 (mt) cc_final: 0.6742 (mm) REVERT: B 447 ARG cc_start: 0.6940 (mtp85) cc_final: 0.6620 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.5828 time to fit residues: 62.4244 Evaluate side-chains 75 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 260 ASN A 270 GLN A 309 HIS A 312 ASN A 358 ASN A 368 HIS A 484 HIS B 69 ASN B 253 ASN B 260 ASN B 270 GLN B 309 HIS B 312 ASN B 358 ASN B 368 HIS B 484 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123987 restraints weight = 7977.686| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.27 r_work: 0.3309 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6718 Z= 0.132 Angle : 0.523 5.900 9134 Z= 0.277 Chirality : 0.040 0.143 1110 Planarity : 0.004 0.041 1108 Dihedral : 4.394 19.570 896 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.13 % Allowed : 9.73 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.28), residues: 840 helix: 0.94 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.24 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 367 TYR 0.015 0.002 TYR B 50 PHE 0.009 0.001 PHE A 361 TRP 0.005 0.001 TRP A 502 HIS 0.007 0.002 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6718) covalent geometry : angle 0.52312 ( 9134) hydrogen bonds : bond 0.03239 ( 448) hydrogen bonds : angle 4.18678 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.275 Fit side-chains REVERT: A 69 ASN cc_start: 0.7217 (t0) cc_final: 0.7014 (t0) REVERT: A 117 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6885 (mt-10) REVERT: A 447 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7025 (ttp-110) REVERT: B 117 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6870 (mt-10) REVERT: B 447 ARG cc_start: 0.7440 (mtp85) cc_final: 0.7033 (ttp-110) outliers start: 16 outliers final: 5 residues processed: 111 average time/residue: 0.4779 time to fit residues: 56.2307 Evaluate side-chains 90 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.0010 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127662 restraints weight = 7953.513| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.28 r_work: 0.3361 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 6718 Z= 0.092 Angle : 0.467 6.008 9134 Z= 0.242 Chirality : 0.037 0.134 1110 Planarity : 0.004 0.038 1108 Dihedral : 3.944 15.747 896 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.07 % Allowed : 12.27 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.28), residues: 840 helix: 1.96 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -1.06 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 448 TYR 0.015 0.002 TYR B 50 PHE 0.010 0.001 PHE A 198 TRP 0.004 0.001 TRP A 531 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 6718) covalent geometry : angle 0.46674 ( 9134) hydrogen bonds : bond 0.02637 ( 448) hydrogen bonds : angle 3.76960 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.235 Fit side-chains REVERT: A 57 LEU cc_start: 0.8208 (mt) cc_final: 0.7530 (tp) REVERT: A 117 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6761 (mt-10) REVERT: A 447 ARG cc_start: 0.7520 (mtp85) cc_final: 0.7163 (ttp-110) REVERT: A 529 LYS cc_start: 0.6283 (ptmm) cc_final: 0.5817 (pttt) REVERT: B 57 LEU cc_start: 0.8213 (mt) cc_final: 0.7526 (tp) REVERT: B 117 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6760 (mt-10) REVERT: B 447 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7158 (ttp-110) REVERT: B 529 LYS cc_start: 0.6294 (ptmm) cc_final: 0.5873 (pttt) outliers start: 8 outliers final: 4 residues processed: 113 average time/residue: 0.5163 time to fit residues: 61.6416 Evaluate side-chains 92 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 0.0870 chunk 19 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.6764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.141933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123011 restraints weight = 7960.720| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.28 r_work: 0.3301 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6718 Z= 0.141 Angle : 0.519 6.535 9134 Z= 0.270 Chirality : 0.040 0.134 1110 Planarity : 0.004 0.039 1108 Dihedral : 4.282 20.591 896 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.93 % Allowed : 11.20 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.28), residues: 840 helix: 2.02 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -0.99 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 367 TYR 0.017 0.002 TYR B 76 PHE 0.010 0.001 PHE B 463 TRP 0.005 0.001 TRP A 287 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6718) covalent geometry : angle 0.51906 ( 9134) hydrogen bonds : bond 0.03110 ( 448) hydrogen bonds : angle 3.82308 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.207 Fit side-chains REVERT: A 117 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6813 (mt-10) REVERT: A 447 ARG cc_start: 0.7437 (mtp85) cc_final: 0.7063 (ttp-110) REVERT: B 117 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6808 (mt-10) REVERT: B 447 ARG cc_start: 0.7422 (mtp85) cc_final: 0.7048 (ttp-110) outliers start: 22 outliers final: 13 residues processed: 106 average time/residue: 0.5371 time to fit residues: 59.9843 Evaluate side-chains 107 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** 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 = 0.3628 r_free = 0.3628 target = 0.143211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124369 restraints weight = 8047.623| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.29 r_work: 0.3319 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6718 Z= 0.119 Angle : 0.496 6.172 9134 Z= 0.256 Chirality : 0.039 0.127 1110 Planarity : 0.004 0.039 1108 Dihedral : 4.144 18.263 896 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.67 % Allowed : 12.53 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.28), residues: 840 helix: 2.31 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.92 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 367 TYR 0.014 0.002 TYR A 76 PHE 0.010 0.001 PHE A 198 TRP 0.004 0.001 TRP A 287 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6718) covalent geometry : angle 0.49581 ( 9134) hydrogen bonds : bond 0.02888 ( 448) hydrogen bonds : angle 3.73694 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.300 Fit side-chains REVERT: A 117 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6779 (mt-10) REVERT: A 256 ILE cc_start: 0.8342 (tt) cc_final: 0.8117 (tt) REVERT: A 447 ARG cc_start: 0.7505 (mtp85) cc_final: 0.7136 (ttp-110) REVERT: B 117 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6775 (mt-10) REVERT: B 256 ILE cc_start: 0.8352 (tt) cc_final: 0.8146 (tt) REVERT: B 447 ARG cc_start: 0.7486 (mtp85) cc_final: 0.7117 (ttp-110) outliers start: 20 outliers final: 13 residues processed: 107 average time/residue: 0.5584 time to fit residues: 63.0116 Evaluate side-chains 108 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 80 optimal weight: 0.0770 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** 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 = 0.3668 r_free = 0.3668 target = 0.146585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.128042 restraints weight = 8008.162| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.29 r_work: 0.3364 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6718 Z= 0.091 Angle : 0.463 6.571 9134 Z= 0.238 Chirality : 0.037 0.116 1110 Planarity : 0.004 0.038 1108 Dihedral : 3.842 15.397 896 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.87 % Allowed : 14.40 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.29), residues: 840 helix: 2.70 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.77 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 367 TYR 0.015 0.002 TYR B 81 PHE 0.011 0.001 PHE B 198 TRP 0.005 0.001 TRP A 531 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 6718) covalent geometry : angle 0.46251 ( 9134) hydrogen bonds : bond 0.02512 ( 448) hydrogen bonds : angle 3.56351 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.258 Fit side-chains REVERT: A 57 LEU cc_start: 0.8239 (mt) cc_final: 0.7548 (tp) REVERT: A 117 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6771 (mt-10) REVERT: A 256 ILE cc_start: 0.8316 (tt) cc_final: 0.8099 (tt) REVERT: A 300 LEU cc_start: 0.6552 (mt) cc_final: 0.6211 (mm) REVERT: A 447 ARG cc_start: 0.7547 (mtp85) cc_final: 0.7194 (ttp-110) REVERT: A 529 LYS cc_start: 0.6248 (ptmm) cc_final: 0.5877 (pttt) REVERT: B 57 LEU cc_start: 0.8243 (mt) cc_final: 0.7553 (tp) REVERT: B 117 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6773 (mt-10) REVERT: B 300 LEU cc_start: 0.6540 (mt) cc_final: 0.6196 (mm) REVERT: B 447 ARG cc_start: 0.7534 (mtp85) cc_final: 0.7182 (ttp-110) REVERT: B 529 LYS cc_start: 0.6355 (ptmm) cc_final: 0.5773 (ttmm) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.5617 time to fit residues: 63.3846 Evaluate side-chains 103 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 50 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.148733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130269 restraints weight = 7966.758| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.29 r_work: 0.3395 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6718 Z= 0.087 Angle : 0.456 6.297 9134 Z= 0.234 Chirality : 0.037 0.113 1110 Planarity : 0.004 0.038 1108 Dihedral : 3.703 14.946 896 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.00 % Allowed : 14.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.85 (0.29), residues: 840 helix: 2.89 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.59 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 367 TYR 0.014 0.001 TYR A 81 PHE 0.011 0.001 PHE A 198 TRP 0.004 0.001 TRP A 502 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00184 ( 6718) covalent geometry : angle 0.45570 ( 9134) hydrogen bonds : bond 0.02396 ( 448) hydrogen bonds : angle 3.48469 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.242 Fit side-chains REVERT: A 57 LEU cc_start: 0.8196 (mt) cc_final: 0.7510 (tp) REVERT: A 66 LYS cc_start: 0.6668 (tptp) cc_final: 0.6438 (tptp) REVERT: A 117 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6773 (mt-10) REVERT: A 256 ILE cc_start: 0.8317 (tt) cc_final: 0.8116 (tt) REVERT: A 367 ARG cc_start: 0.7938 (mmm-85) cc_final: 0.7719 (mmm-85) REVERT: A 447 ARG cc_start: 0.7518 (mtp85) cc_final: 0.7134 (ttp-110) REVERT: A 529 LYS cc_start: 0.6118 (ptmm) cc_final: 0.5561 (ttmm) REVERT: B 57 LEU cc_start: 0.8202 (mt) cc_final: 0.7512 (tp) REVERT: B 117 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6761 (mt-10) REVERT: B 447 ARG cc_start: 0.7560 (mtp85) cc_final: 0.7175 (ttp-110) REVERT: B 529 LYS cc_start: 0.6400 (ptmm) cc_final: 0.5773 (ttmm) outliers start: 15 outliers final: 8 residues processed: 105 average time/residue: 0.5295 time to fit residues: 58.8181 Evaluate side-chains 94 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS B 69 ASN ** B 244 ASN ** 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 = 0.3630 r_free = 0.3630 target = 0.143148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124152 restraints weight = 8017.139| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.31 r_work: 0.3320 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6718 Z= 0.134 Angle : 0.517 6.814 9134 Z= 0.266 Chirality : 0.040 0.124 1110 Planarity : 0.004 0.038 1108 Dihedral : 4.130 17.906 896 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.60 % Allowed : 15.33 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.29), residues: 840 helix: 2.55 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.64 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 367 TYR 0.016 0.002 TYR B 76 PHE 0.010 0.001 PHE B 463 TRP 0.006 0.001 TRP B 45 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6718) covalent geometry : angle 0.51661 ( 9134) hydrogen bonds : bond 0.02983 ( 448) hydrogen bonds : angle 3.70729 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.269 Fit side-chains REVERT: A 57 LEU cc_start: 0.8224 (mt) cc_final: 0.7516 (tp) REVERT: A 66 LYS cc_start: 0.6751 (tptp) cc_final: 0.6542 (tptp) REVERT: A 117 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6759 (mt-10) REVERT: A 447 ARG cc_start: 0.7504 (mtp85) cc_final: 0.7146 (ttp-110) REVERT: B 57 LEU cc_start: 0.8202 (mt) cc_final: 0.7496 (tp) REVERT: B 117 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6749 (mt-10) REVERT: B 447 ARG cc_start: 0.7450 (mtp85) cc_final: 0.7080 (ttp-110) outliers start: 12 outliers final: 8 residues processed: 97 average time/residue: 0.6154 time to fit residues: 62.6041 Evaluate side-chains 97 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS ** B 244 ASN ** 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 = 0.3668 r_free = 0.3668 target = 0.146647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127956 restraints weight = 8006.977| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.30 r_work: 0.3360 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6718 Z= 0.096 Angle : 0.478 6.349 9134 Z= 0.246 Chirality : 0.038 0.118 1110 Planarity : 0.004 0.038 1108 Dihedral : 3.865 15.876 896 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.47 % Allowed : 16.00 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.75 (0.29), residues: 840 helix: 2.80 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.61 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.015 0.002 TYR B 81 PHE 0.011 0.001 PHE B 198 TRP 0.004 0.001 TRP A 502 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 6718) covalent geometry : angle 0.47755 ( 9134) hydrogen bonds : bond 0.02579 ( 448) hydrogen bonds : angle 3.56691 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.233 Fit side-chains REVERT: A 57 LEU cc_start: 0.8185 (mt) cc_final: 0.7523 (tp) REVERT: A 117 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6782 (mt-10) REVERT: A 447 ARG cc_start: 0.7529 (mtp85) cc_final: 0.7181 (ttp-110) REVERT: A 529 LYS cc_start: 0.6337 (ptmm) cc_final: 0.5800 (pttt) REVERT: B 57 LEU cc_start: 0.8185 (mt) cc_final: 0.7512 (tp) REVERT: B 117 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6768 (mt-10) REVERT: B 447 ARG cc_start: 0.7482 (mtp85) cc_final: 0.7130 (ttp-110) REVERT: B 529 LYS cc_start: 0.6414 (ptmm) cc_final: 0.5640 (ttmm) outliers start: 11 outliers final: 8 residues processed: 94 average time/residue: 0.5123 time to fit residues: 50.6026 Evaluate side-chains 95 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 0.0470 chunk 57 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.128963 restraints weight = 7975.916| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.16 r_work: 0.3356 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6718 Z= 0.104 Angle : 0.487 6.465 9134 Z= 0.250 Chirality : 0.038 0.114 1110 Planarity : 0.004 0.038 1108 Dihedral : 3.905 16.081 896 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.73 % Allowed : 15.87 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.29), residues: 840 helix: 2.78 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.62 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.014 0.002 TYR A 81 PHE 0.009 0.001 PHE A 198 TRP 0.004 0.001 TRP A 502 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 6718) covalent geometry : angle 0.48727 ( 9134) hydrogen bonds : bond 0.02653 ( 448) hydrogen bonds : angle 3.57965 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.153 Fit side-chains REVERT: A 57 LEU cc_start: 0.8210 (mt) cc_final: 0.7617 (tp) REVERT: A 117 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6895 (mt-10) REVERT: A 447 ARG cc_start: 0.7549 (mtp85) cc_final: 0.7209 (ttp-110) REVERT: A 529 LYS cc_start: 0.6382 (ptmm) cc_final: 0.5856 (pttt) REVERT: B 57 LEU cc_start: 0.8198 (mt) cc_final: 0.7602 (tp) REVERT: B 117 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6873 (mt-10) REVERT: B 447 ARG cc_start: 0.7596 (mtp85) cc_final: 0.7271 (ttp-110) REVERT: B 529 LYS cc_start: 0.6484 (ptmm) cc_final: 0.5735 (ttmm) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 0.4945 time to fit residues: 48.4133 Evaluate side-chains 95 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 0.0570 chunk 53 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 244 ASN ** 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 = 0.3692 r_free = 0.3692 target = 0.148757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130307 restraints weight = 7913.842| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.29 r_work: 0.3387 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6718 Z= 0.091 Angle : 0.469 6.249 9134 Z= 0.241 Chirality : 0.037 0.112 1110 Planarity : 0.004 0.038 1108 Dihedral : 3.761 14.971 896 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.20 % Allowed : 16.40 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.29), residues: 840 helix: 2.92 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.62 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.017 0.002 TYR B 81 PHE 0.011 0.001 PHE A 198 TRP 0.004 0.001 TRP B 502 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 6718) covalent geometry : angle 0.46865 ( 9134) hydrogen bonds : bond 0.02465 ( 448) hydrogen bonds : angle 3.50773 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.21 seconds wall clock time: 37 minutes 53.58 seconds (2273.58 seconds total)