Starting phenix.real_space_refine on Thu Jun 5 15:26:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9t_37381/06_2025/8w9t_37381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9t_37381/06_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_37381/06_2025/8w9t_37381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9t_37381/06_2025/8w9t_37381.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9t_37381/06_2025/8w9t_37381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9t_37381/06_2025/8w9t_37381.cif" } resolution = 2.6 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= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.25, per 1000 atoms: 0.65 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: 1.65 Conformation dependent library (CDL) restraints added in 897.1 milliseconds 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: 0.67 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: 1.76 Time building geometry restraints manager: 1.92 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: 0.03 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.670 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- 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 (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: -1.88 (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 TRP 0.007 0.001 TRP A 287 HIS 0.007 0.002 HIS B 368 PHE 0.011 0.001 PHE A 361 TYR 0.015 0.002 TYR B 50 ARG 0.004 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.13137 ( 448) hydrogen bonds : angle 6.20942 ( 1296) covalent geometry : bond 0.00451 ( 6718) covalent geometry : angle 0.60119 ( 9134) *********************** 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 : 0.852 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: 1.1646 time to fit residues: 125.3518 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 : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123797 restraints weight = 7918.663| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.14 r_work: 0.3294 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6718 Z= 0.159 Angle : 0.555 6.280 9134 Z= 0.293 Chirality : 0.041 0.149 1110 Planarity : 0.005 0.042 1108 Dihedral : 4.570 21.429 896 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.13 % Allowed : 9.60 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.27), residues: 840 helix: 0.77 (0.20), residues: 586 sheet: None (None), residues: 0 loop : -1.24 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 287 HIS 0.007 0.002 HIS A 368 PHE 0.011 0.002 PHE B 463 TYR 0.015 0.002 TYR B 50 ARG 0.003 0.001 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 448) hydrogen bonds : angle 4.26071 ( 1296) covalent geometry : bond 0.00359 ( 6718) covalent geometry : angle 0.55454 ( 9134) *********************** 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 : 0.877 Fit side-chains REVERT: A 69 ASN cc_start: 0.7183 (t0) cc_final: 0.6937 (t0) REVERT: A 117 GLU cc_start: 0.7246 (tm-30) cc_final: 0.7018 (mt-10) REVERT: A 447 ARG cc_start: 0.7372 (mtp85) cc_final: 0.6970 (ttp-110) REVERT: B 69 ASN cc_start: 0.7396 (t0) cc_final: 0.7190 (t0) REVERT: B 117 GLU cc_start: 0.7240 (tm-30) cc_final: 0.7019 (mt-10) REVERT: B 447 ARG cc_start: 0.7375 (mtp85) cc_final: 0.6973 (ttp-110) outliers start: 16 outliers final: 5 residues processed: 110 average time/residue: 1.3132 time to fit residues: 153.3668 Evaluate side-chains 87 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 15 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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** B 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127363 restraints weight = 8022.121| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.28 r_work: 0.3358 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6718 Z= 0.094 Angle : 0.468 6.011 9134 Z= 0.244 Chirality : 0.037 0.136 1110 Planarity : 0.004 0.039 1108 Dihedral : 3.975 15.678 896 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.33 % Allowed : 11.73 % Favored : 86.93 % 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: 1.57 (0.28), residues: 840 helix: 1.91 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -1.09 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 531 HIS 0.002 0.001 HIS A 368 PHE 0.011 0.001 PHE A 198 TYR 0.015 0.002 TYR B 50 ARG 0.001 0.000 ARG B 448 Details of bonding type rmsd hydrogen bonds : bond 0.02638 ( 448) hydrogen bonds : angle 3.77109 ( 1296) covalent geometry : bond 0.00201 ( 6718) covalent geometry : angle 0.46776 ( 9134) *********************** 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: 10 poor density : 103 time to evaluate : 0.921 Fit side-chains REVERT: A 57 LEU cc_start: 0.8216 (mt) cc_final: 0.7543 (tp) REVERT: A 117 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6781 (mt-10) REVERT: A 447 ARG cc_start: 0.7507 (mtp85) cc_final: 0.7149 (ttp-110) REVERT: B 117 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6786 (mt-10) REVERT: B 447 ARG cc_start: 0.7509 (mtp85) cc_final: 0.7150 (ttp-110) REVERT: B 529 LYS cc_start: 0.6414 (ptmm) cc_final: 0.5961 (pttp) outliers start: 10 outliers final: 4 residues processed: 111 average time/residue: 1.8142 time to fit residues: 213.7249 Evaluate side-chains 93 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 29 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.141884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123068 restraints weight = 8036.243| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.28 r_work: 0.3299 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1717 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= 0.145 Angle : 0.524 6.633 9134 Z= 0.273 Chirality : 0.040 0.131 1110 Planarity : 0.004 0.041 1108 Dihedral : 4.289 20.515 896 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.07 % Allowed : 11.47 % Favored : 85.47 % 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: 1.68 (0.28), residues: 840 helix: 2.01 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.06 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 287 HIS 0.005 0.001 HIS A 368 PHE 0.010 0.001 PHE A 463 TYR 0.017 0.002 TYR B 76 ARG 0.006 0.001 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 448) hydrogen bonds : angle 3.82843 ( 1296) covalent geometry : bond 0.00328 ( 6718) covalent geometry : angle 0.52443 ( 9134) *********************** 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 113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 1.393 Fit side-chains REVERT: A 117 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6811 (mt-10) REVERT: A 447 ARG cc_start: 0.7437 (mtp85) cc_final: 0.7063 (ttp-110) REVERT: B 69 ASN cc_start: 0.7252 (t0) cc_final: 0.7044 (t0) REVERT: B 117 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6810 (mt-10) REVERT: B 447 ARG cc_start: 0.7420 (mtp85) cc_final: 0.7045 (ttp-110) outliers start: 23 outliers final: 13 residues processed: 105 average time/residue: 2.1940 time to fit residues: 244.9835 Evaluate side-chains 102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.793 ------------------------------------------------------------------------------- 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 42 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.144545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125905 restraints weight = 7895.760| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.27 r_work: 0.3340 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6718 Z= 0.104 Angle : 0.482 5.871 9134 Z= 0.250 Chirality : 0.038 0.122 1110 Planarity : 0.004 0.040 1108 Dihedral : 4.007 16.603 896 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.53 % Allowed : 13.20 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.29), residues: 840 helix: 2.43 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.91 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 502 HIS 0.004 0.001 HIS B 368 PHE 0.011 0.001 PHE A 198 TYR 0.014 0.002 TYR B 50 ARG 0.005 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.02702 ( 448) hydrogen bonds : angle 3.66750 ( 1296) covalent geometry : bond 0.00229 ( 6718) covalent geometry : angle 0.48243 ( 9134) *********************** 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 113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 3.169 Fit side-chains REVERT: A 57 LEU cc_start: 0.8202 (mt) cc_final: 0.7519 (tp) REVERT: A 117 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6802 (mt-10) REVERT: A 256 ILE cc_start: 0.8358 (tt) cc_final: 0.8138 (tt) REVERT: A 447 ARG cc_start: 0.7532 (mtp85) cc_final: 0.7164 (ttp-110) REVERT: A 529 LYS cc_start: 0.6556 (ptmm) cc_final: 0.5947 (tttp) REVERT: B 57 LEU cc_start: 0.8216 (mt) cc_final: 0.7517 (tp) REVERT: B 117 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6796 (mt-10) REVERT: B 256 ILE cc_start: 0.8348 (tt) cc_final: 0.8128 (tt) REVERT: B 447 ARG cc_start: 0.7473 (mtp85) cc_final: 0.7113 (ttp-110) outliers start: 19 outliers final: 11 residues processed: 105 average time/residue: 1.7609 time to fit residues: 195.0208 Evaluate side-chains 102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.146061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127435 restraints weight = 7943.784| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.28 r_work: 0.3367 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6718 Z= 0.096 Angle : 0.467 5.473 9134 Z= 0.242 Chirality : 0.038 0.117 1110 Planarity : 0.004 0.040 1108 Dihedral : 3.847 15.028 896 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.00 % Allowed : 14.40 % Favored : 83.60 % 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: 2.53 (0.29), residues: 840 helix: 2.66 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.76 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 502 HIS 0.003 0.001 HIS A 368 PHE 0.011 0.001 PHE A 198 TYR 0.015 0.002 TYR B 81 ARG 0.007 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.02550 ( 448) hydrogen bonds : angle 3.56523 ( 1296) covalent geometry : bond 0.00207 ( 6718) covalent geometry : angle 0.46711 ( 9134) *********************** 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 108 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.749 Fit side-chains REVERT: A 57 LEU cc_start: 0.8238 (mt) cc_final: 0.7562 (tp) REVERT: A 117 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6759 (mt-10) REVERT: A 256 ILE cc_start: 0.8328 (tt) cc_final: 0.8124 (tt) REVERT: A 447 ARG cc_start: 0.7529 (mtp85) cc_final: 0.7180 (ttp-110) REVERT: A 529 LYS cc_start: 0.6440 (ptmm) cc_final: 0.5890 (tttp) REVERT: B 57 LEU cc_start: 0.8248 (mt) cc_final: 0.7568 (tp) REVERT: B 117 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6754 (mt-10) REVERT: B 256 ILE cc_start: 0.8334 (tt) cc_final: 0.8134 (tt) REVERT: B 447 ARG cc_start: 0.7529 (mtp85) cc_final: 0.7177 (ttp-110) outliers start: 15 outliers final: 12 residues processed: 102 average time/residue: 1.0653 time to fit residues: 115.4884 Evaluate side-chains 101 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** B 487 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125691 restraints weight = 7917.662| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.29 r_work: 0.3341 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6718 Z= 0.110 Angle : 0.486 5.778 9134 Z= 0.251 Chirality : 0.038 0.116 1110 Planarity : 0.004 0.040 1108 Dihedral : 3.970 16.009 896 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.13 % Allowed : 14.67 % Favored : 83.20 % 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: 2.49 (0.29), residues: 840 helix: 2.61 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.71 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 502 HIS 0.004 0.001 HIS A 368 PHE 0.010 0.001 PHE B 198 TYR 0.013 0.002 TYR A 76 ARG 0.006 0.001 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.02723 ( 448) hydrogen bonds : angle 3.61651 ( 1296) covalent geometry : bond 0.00243 ( 6718) covalent geometry : angle 0.48604 ( 9134) *********************** 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 102 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.864 Fit side-chains REVERT: A 57 LEU cc_start: 0.8202 (mt) cc_final: 0.7521 (tp) REVERT: A 117 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6790 (mt-10) REVERT: A 447 ARG cc_start: 0.7553 (mtp85) cc_final: 0.7197 (ttp-110) REVERT: A 529 LYS cc_start: 0.6470 (ptmm) cc_final: 0.5815 (mttm) REVERT: B 57 LEU cc_start: 0.8196 (mt) cc_final: 0.7514 (tp) REVERT: B 117 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6790 (mt-10) REVERT: B 447 ARG cc_start: 0.7540 (mtp85) cc_final: 0.7182 (ttp-110) REVERT: B 529 LYS cc_start: 0.6452 (ptmm) cc_final: 0.5868 (pttp) outliers start: 16 outliers final: 11 residues processed: 96 average time/residue: 1.1053 time to fit residues: 112.2602 Evaluate side-chains 99 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 0.0000 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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** B 487 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126774 restraints weight = 7958.713| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.29 r_work: 0.3352 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6718 Z= 0.101 Angle : 0.475 5.556 9134 Z= 0.246 Chirality : 0.038 0.117 1110 Planarity : 0.004 0.040 1108 Dihedral : 3.887 15.469 896 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.00 % Allowed : 14.40 % Favored : 83.60 % 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: 2.62 (0.29), residues: 840 helix: 2.71 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.65 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 502 HIS 0.004 0.001 HIS A 368 PHE 0.011 0.001 PHE A 198 TYR 0.014 0.002 TYR B 81 ARG 0.006 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.02604 ( 448) hydrogen bonds : angle 3.58026 ( 1296) covalent geometry : bond 0.00221 ( 6718) covalent geometry : angle 0.47502 ( 9134) *********************** 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 105 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.728 Fit side-chains REVERT: A 57 LEU cc_start: 0.8192 (mt) cc_final: 0.7527 (tp) REVERT: A 117 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6746 (mt-10) REVERT: A 447 ARG cc_start: 0.7519 (mtp85) cc_final: 0.7171 (ttp-110) REVERT: A 529 LYS cc_start: 0.6433 (ptmm) cc_final: 0.6035 (tttp) REVERT: B 57 LEU cc_start: 0.8201 (mt) cc_final: 0.7532 (tp) REVERT: B 117 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6772 (mt-10) REVERT: B 447 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7166 (ttp-110) REVERT: B 529 LYS cc_start: 0.6396 (ptmm) cc_final: 0.5693 (ttmm) outliers start: 15 outliers final: 11 residues processed: 97 average time/residue: 1.1237 time to fit residues: 115.3586 Evaluate side-chains 97 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 68 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** B 487 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128826 restraints weight = 8028.873| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.31 r_work: 0.3382 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6718 Z= 0.091 Angle : 0.459 5.260 9134 Z= 0.237 Chirality : 0.038 0.114 1110 Planarity : 0.004 0.040 1108 Dihedral : 3.749 14.609 896 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.47 % Allowed : 15.07 % Favored : 83.47 % 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: 2.82 (0.29), residues: 840 helix: 2.87 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.60 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 502 HIS 0.003 0.001 HIS A 368 PHE 0.011 0.001 PHE A 198 TYR 0.016 0.002 TYR A 81 ARG 0.003 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.02435 ( 448) hydrogen bonds : angle 3.50458 ( 1296) covalent geometry : bond 0.00195 ( 6718) covalent geometry : angle 0.45867 ( 9134) *********************** 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 105 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.787 Fit side-chains REVERT: A 57 LEU cc_start: 0.8230 (mt) cc_final: 0.7565 (tp) REVERT: A 117 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6742 (mt-10) REVERT: A 256 ILE cc_start: 0.8334 (tt) cc_final: 0.8111 (tt) REVERT: A 300 LEU cc_start: 0.6352 (mt) cc_final: 0.5999 (mm) REVERT: A 447 ARG cc_start: 0.7506 (mtp85) cc_final: 0.7168 (ttp-110) REVERT: A 529 LYS cc_start: 0.6434 (ptmm) cc_final: 0.6035 (tttp) REVERT: B 57 LEU cc_start: 0.8225 (mt) cc_final: 0.7554 (tp) REVERT: B 66 LYS cc_start: 0.6671 (tptp) cc_final: 0.6467 (tptp) REVERT: B 117 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6750 (mt-10) REVERT: B 256 ILE cc_start: 0.8344 (tt) cc_final: 0.8123 (tt) REVERT: B 447 ARG cc_start: 0.7504 (mtp85) cc_final: 0.7165 (ttp-110) REVERT: B 529 LYS cc_start: 0.6232 (ptmm) cc_final: 0.5618 (ttmm) outliers start: 11 outliers final: 11 residues processed: 101 average time/residue: 1.0965 time to fit residues: 117.4129 Evaluate side-chains 97 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 201 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 201 ILE 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 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.142575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124894 restraints weight = 7975.960| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.17 r_work: 0.3316 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1965 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= 0.147 Angle : 0.537 6.181 9134 Z= 0.279 Chirality : 0.041 0.161 1110 Planarity : 0.004 0.041 1108 Dihedral : 4.202 17.784 896 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.73 % Allowed : 15.47 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.37 (0.28), residues: 840 helix: 2.50 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 45 HIS 0.004 0.001 HIS B 368 PHE 0.010 0.001 PHE A 463 TYR 0.016 0.002 TYR A 76 ARG 0.002 0.000 ARG A 519 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 448) hydrogen bonds : angle 3.75830 ( 1296) covalent geometry : bond 0.00334 ( 6718) covalent geometry : angle 0.53740 ( 9134) ********************** 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 104 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.921 Fit side-chains REVERT: A 117 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6798 (mt-10) REVERT: A 256 ILE cc_start: 0.8357 (tt) cc_final: 0.8127 (tt) REVERT: A 447 ARG cc_start: 0.7432 (mtp85) cc_final: 0.7062 (ttp-110) REVERT: B 66 LYS cc_start: 0.6711 (tptp) cc_final: 0.6495 (tptp) REVERT: B 117 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6784 (mt-10) REVERT: B 256 ILE cc_start: 0.8361 (tt) cc_final: 0.8131 (tt) REVERT: B 447 ARG cc_start: 0.7423 (mtp85) cc_final: 0.7052 (ttp-110) outliers start: 13 outliers final: 9 residues processed: 98 average time/residue: 1.1629 time to fit residues: 120.3067 Evaluate side-chains 96 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 45 optimal weight: 0.0070 chunk 31 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 0.3980 chunk 34 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130378 restraints weight = 8006.610| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.29 r_work: 0.3395 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6718 Z= 0.090 Angle : 0.466 6.385 9134 Z= 0.241 Chirality : 0.038 0.120 1110 Planarity : 0.004 0.039 1108 Dihedral : 3.783 15.701 896 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.07 % Allowed : 16.80 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.83 (0.29), residues: 840 helix: 2.90 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 531 HIS 0.002 0.001 HIS A 368 PHE 0.011 0.001 PHE B 198 TYR 0.015 0.002 TYR A 81 ARG 0.003 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.02428 ( 448) hydrogen bonds : angle 3.55231 ( 1296) covalent geometry : bond 0.00192 ( 6718) covalent geometry : angle 0.46620 ( 9134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5799.94 seconds wall clock time: 104 minutes 56.43 seconds (6296.43 seconds total)