Starting phenix.real_space_refine on Wed Mar 4 06:38:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wcc_21606/03_2026/6wcc_21606.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wcc_21606/03_2026/6wcc_21606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wcc_21606/03_2026/6wcc_21606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wcc_21606/03_2026/6wcc_21606.map" model { file = "/net/cci-nas-00/data/ceres_data/6wcc_21606/03_2026/6wcc_21606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wcc_21606/03_2026/6wcc_21606.cif" } resolution = 3.24 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cs 5 16.47 5 S 38 5.16 5 C 3758 2.51 5 N 940 2.21 5 O 980 1.98 5 H 5908 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11629 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5806 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5806 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 2.35, per 1000 atoms: 0.20 Number of scatterers: 11629 At special positions: 0 Unit cell: (107.712, 66.368, 78.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cs 5 54.66 S 38 16.00 O 980 8.00 N 940 7.00 C 3758 6.00 H 5908 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 331.7 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 86.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 67 through 103 removed outlier: 4.180A pdb=" N GLN A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 137 through 164 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 257 through 284 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 333 removed outlier: 3.839A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 3.624A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.544A pdb=" N ALA A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 400 removed outlier: 3.912A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 4.951A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'B' and resid 33 through 50 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 67 through 103 removed outlier: 4.180A pdb=" N GLN B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 137 through 164 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 257 through 284 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 298 through 333 removed outlier: 3.840A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 3.624A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.544A pdb=" N ALA B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 400 removed outlier: 3.912A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 4.952A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 462 hydrogen bonds defined for protein. 1368 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: 2.58 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5890 1.03 - 1.23: 18 1.23 - 1.42: 2386 1.42 - 1.61: 3394 1.61 - 1.81: 58 Bond restraints: 11746 Sorted by residual: bond pdb=" CG LEU B 470 " pdb=" CD1 LEU B 470 " ideal model delta sigma weight residual 1.521 1.559 -0.038 3.30e-02 9.18e+02 1.31e+00 bond pdb=" CG PHE A 295 " pdb=" CD2 PHE A 295 " ideal model delta sigma weight residual 1.384 1.360 0.024 2.10e-02 2.27e+03 1.26e+00 bond pdb=" CG LEU A 470 " pdb=" CD1 LEU A 470 " ideal model delta sigma weight residual 1.521 1.558 -0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CG PHE B 295 " pdb=" CD2 PHE B 295 " ideal model delta sigma weight residual 1.384 1.361 0.023 2.10e-02 2.27e+03 1.17e+00 bond pdb=" CB GLU B 59 " pdb=" CG GLU B 59 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.96e-01 ... (remaining 11741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 21172 2.12 - 4.24: 111 4.24 - 6.37: 8 6.37 - 8.49: 3 8.49 - 10.61: 2 Bond angle restraints: 21296 Sorted by residual: angle pdb=" CG LEU A 470 " pdb=" CD2 LEU A 470 " pdb="HD23 LEU A 470 " ideal model delta sigma weight residual 109.00 98.39 10.61 3.00e+00 1.11e-01 1.25e+01 angle pdb="HD21 LEU A 470 " pdb=" CD2 LEU A 470 " pdb="HD23 LEU A 470 " ideal model delta sigma weight residual 110.00 100.10 9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CG LEU A 470 " pdb=" CD2 LEU A 470 " pdb="HD21 LEU A 470 " ideal model delta sigma weight residual 109.00 117.41 -8.41 3.00e+00 1.11e-01 7.85e+00 angle pdb=" CD2 LEU B 470 " pdb=" CG LEU B 470 " pdb=" HG LEU B 470 " ideal model delta sigma weight residual 108.00 100.28 7.72 3.00e+00 1.11e-01 6.63e+00 angle pdb="HD22 LEU A 470 " pdb=" CD2 LEU A 470 " pdb="HD23 LEU A 470 " ideal model delta sigma weight residual 110.00 116.89 -6.89 3.00e+00 1.11e-01 5.28e+00 ... (remaining 21291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 4918 16.97 - 33.93: 428 33.93 - 50.90: 118 50.90 - 67.86: 58 67.86 - 84.83: 6 Dihedral angle restraints: 5528 sinusoidal: 2936 harmonic: 2592 Sorted by residual: dihedral pdb=" CA ASP A 283 " pdb=" C ASP A 283 " pdb=" N ASN A 284 " pdb=" CA ASN A 284 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP B 283 " pdb=" C ASP B 283 " pdb=" N ASN B 284 " pdb=" CA ASN B 284 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASN B 284 " pdb=" CB ASN B 284 " pdb=" CG ASN B 284 " pdb=" OD1 ASN B 284 " ideal model delta sinusoidal sigma weight residual -90.00 -162.72 72.72 2 2.00e+01 2.50e-03 1.09e+01 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 721 0.027 - 0.053: 128 0.053 - 0.080: 84 0.080 - 0.107: 34 0.107 - 0.134: 11 Chirality restraints: 978 Sorted by residual: chirality pdb=" CG LEU A 470 " pdb=" CB LEU A 470 " pdb=" CD1 LEU A 470 " pdb=" CD2 LEU A 470 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CG LEU B 470 " pdb=" CB LEU B 470 " pdb=" CD1 LEU B 470 " pdb=" CD2 LEU B 470 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL A 285 " pdb=" N VAL A 285 " pdb=" C VAL A 285 " pdb=" CB VAL A 285 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 975 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 295 " -0.028 2.00e-02 2.50e+03 1.82e-02 9.89e+00 pdb=" CG PHE A 295 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 295 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 295 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 295 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 295 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 295 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 295 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE A 295 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE A 295 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 295 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 295 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 295 " 0.022 2.00e-02 2.50e+03 1.78e-02 9.48e+00 pdb=" CG PHE B 295 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE B 295 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 295 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 295 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 295 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 295 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE B 295 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 295 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 295 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 295 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE B 295 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 123 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 124 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " -0.021 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.60: 12042 2.60 - 3.41: 46823 3.41 - 4.23: 62751 4.23 - 5.04: 110077 5.04 - 5.86: 145341 Nonbonded interactions: 377034 Sorted by model distance: nonbonded pdb=" O LEU B 123 " pdb=" HG1 THR B 126 " model vdw 1.784 2.450 nonbonded pdb=" O LEU A 123 " pdb=" HG1 THR A 126 " model vdw 1.784 2.450 nonbonded pdb=" OD1 ASP A 266 " pdb="HH21 ARG B 35 " model vdw 1.812 2.450 nonbonded pdb=" O ALA A 93 " pdb=" HG1 THR A 96 " model vdw 1.812 2.450 nonbonded pdb=" O ALA B 93 " pdb=" HG1 THR B 96 " model vdw 1.813 2.450 ... (remaining 377029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 30 through 702) 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: 0.010 Normalize map: mean=0, sd=1: 0.060 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: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.950 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.003 0.038 5838 Z= 0.134 Angle : 0.510 4.479 7956 Z= 0.278 Chirality : 0.033 0.134 978 Planarity : 0.004 0.038 976 Dihedral : 15.734 84.831 2040 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.26 % Allowed : 10.32 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.28), residues: 726 helix: 1.59 (0.19), residues: 590 sheet: None (None), residues: 0 loop : -1.76 (0.44), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 72 TYR 0.008 0.001 TYR A 313 PHE 0.053 0.001 PHE A 295 TRP 0.006 0.001 TRP A 394 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5838) covalent geometry : angle 0.51011 ( 7956) hydrogen bonds : bond 0.10621 ( 462) hydrogen bonds : angle 4.28443 ( 1368) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 418 LEU cc_start: 0.8247 (tp) cc_final: 0.7995 (mp) outliers start: 14 outliers final: 12 residues processed: 143 average time/residue: 0.1804 time to fit residues: 33.0293 Evaluate side-chains 103 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.0030 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.172964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124942 restraints weight = 9139.767| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.59 r_work: 0.3120 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5838 Z= 0.123 Angle : 0.500 5.569 7956 Z= 0.250 Chirality : 0.034 0.127 978 Planarity : 0.004 0.045 976 Dihedral : 7.899 70.457 804 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.74 % Allowed : 14.84 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.60 (0.30), residues: 726 helix: 3.13 (0.20), residues: 586 sheet: None (None), residues: 0 loop : -1.19 (0.47), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.011 0.002 TYR B 160 PHE 0.017 0.001 PHE A 99 TRP 0.012 0.001 TRP B 394 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5838) covalent geometry : angle 0.49986 ( 7956) hydrogen bonds : bond 0.04743 ( 462) hydrogen bonds : angle 3.67944 ( 1368) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7930 (mtt90) REVERT: A 117 MET cc_start: 0.7949 (mmt) cc_final: 0.7717 (mmt) REVERT: B 77 ARG cc_start: 0.8215 (mtt90) cc_final: 0.7933 (mtt90) REVERT: B 418 LEU cc_start: 0.8449 (tp) cc_final: 0.8035 (mp) outliers start: 17 outliers final: 11 residues processed: 120 average time/residue: 0.1753 time to fit residues: 27.4129 Evaluate side-chains 107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.168803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.120016 restraints weight = 9504.353| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.63 r_work: 0.3073 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5838 Z= 0.149 Angle : 0.500 5.617 7956 Z= 0.257 Chirality : 0.035 0.129 978 Planarity : 0.004 0.048 976 Dihedral : 6.805 56.670 800 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.58 % Allowed : 15.65 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.99 (0.31), residues: 726 helix: 3.30 (0.20), residues: 598 sheet: None (None), residues: 0 loop : -0.91 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.017 0.002 TYR B 125 PHE 0.017 0.001 PHE A 99 TRP 0.009 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5838) covalent geometry : angle 0.50031 ( 7956) hydrogen bonds : bond 0.04773 ( 462) hydrogen bonds : angle 3.61471 ( 1368) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.6086 (tp40) cc_final: 0.5761 (tm-30) REVERT: A 77 ARG cc_start: 0.8169 (mtt90) cc_final: 0.7940 (mtt90) REVERT: B 71 GLN cc_start: 0.6148 (tp40) cc_final: 0.5759 (tm-30) REVERT: B 117 MET cc_start: 0.8291 (mmp) cc_final: 0.8053 (mmt) outliers start: 16 outliers final: 13 residues processed: 111 average time/residue: 0.1965 time to fit residues: 28.0372 Evaluate side-chains 100 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.167858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.119018 restraints weight = 9930.737| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.65 r_work: 0.3062 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5838 Z= 0.140 Angle : 0.486 4.016 7956 Z= 0.248 Chirality : 0.035 0.121 978 Planarity : 0.004 0.047 976 Dihedral : 6.209 55.755 800 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.42 % Allowed : 15.65 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.04 (0.31), residues: 726 helix: 3.32 (0.20), residues: 598 sheet: None (None), residues: 0 loop : -0.85 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.014 0.002 TYR A 125 PHE 0.015 0.001 PHE B 99 TRP 0.010 0.001 TRP B 394 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5838) covalent geometry : angle 0.48594 ( 7956) hydrogen bonds : bond 0.04505 ( 462) hydrogen bonds : angle 3.56790 ( 1368) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.6204 (tp40) cc_final: 0.5794 (tm-30) REVERT: A 77 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7918 (mtt90) REVERT: A 160 TYR cc_start: 0.8807 (t80) cc_final: 0.8521 (t80) REVERT: B 71 GLN cc_start: 0.6226 (tp40) cc_final: 0.5718 (tm-30) REVERT: B 77 ARG cc_start: 0.8188 (mtt90) cc_final: 0.7948 (mtt90) outliers start: 15 outliers final: 12 residues processed: 108 average time/residue: 0.1805 time to fit residues: 25.7385 Evaluate side-chains 107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.168705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119780 restraints weight = 10114.799| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.66 r_work: 0.3070 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5838 Z= 0.120 Angle : 0.470 3.985 7956 Z= 0.238 Chirality : 0.034 0.120 978 Planarity : 0.004 0.047 976 Dihedral : 5.189 54.470 790 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.26 % Allowed : 15.48 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.17 (0.31), residues: 726 helix: 3.42 (0.20), residues: 598 sheet: None (None), residues: 0 loop : -0.84 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.013 0.002 TYR A 125 PHE 0.014 0.001 PHE B 99 TRP 0.011 0.001 TRP B 394 HIS 0.006 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 5838) covalent geometry : angle 0.46968 ( 7956) hydrogen bonds : bond 0.04264 ( 462) hydrogen bonds : angle 3.50837 ( 1368) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.6217 (tp40) cc_final: 0.5832 (tm-30) REVERT: A 160 TYR cc_start: 0.8831 (t80) cc_final: 0.8575 (t80) REVERT: B 71 GLN cc_start: 0.6212 (tp40) cc_final: 0.5716 (tm-30) REVERT: B 77 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7876 (mtt90) REVERT: B 117 MET cc_start: 0.8241 (mmp) cc_final: 0.8031 (mmt) outliers start: 14 outliers final: 12 residues processed: 107 average time/residue: 0.1784 time to fit residues: 25.1235 Evaluate side-chains 102 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.165408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114843 restraints weight = 9665.705| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.67 r_work: 0.3003 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5838 Z= 0.195 Angle : 0.520 4.390 7956 Z= 0.272 Chirality : 0.036 0.129 978 Planarity : 0.004 0.046 976 Dihedral : 5.195 55.276 790 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.42 % Allowed : 15.16 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.75 (0.31), residues: 726 helix: 3.10 (0.20), residues: 598 sheet: None (None), residues: 0 loop : -0.82 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 35 TYR 0.016 0.002 TYR B 125 PHE 0.016 0.002 PHE B 99 TRP 0.008 0.002 TRP B 394 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 5838) covalent geometry : angle 0.51996 ( 7956) hydrogen bonds : bond 0.05074 ( 462) hydrogen bonds : angle 3.70659 ( 1368) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.6327 (tp40) cc_final: 0.5796 (tm-30) REVERT: A 160 TYR cc_start: 0.8940 (t80) cc_final: 0.8594 (t80) REVERT: B 71 GLN cc_start: 0.6304 (tp40) cc_final: 0.5765 (tm-30) REVERT: B 117 MET cc_start: 0.8227 (mmp) cc_final: 0.8005 (mmt) outliers start: 15 outliers final: 15 residues processed: 105 average time/residue: 0.1849 time to fit residues: 25.5663 Evaluate side-chains 104 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.168025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117959 restraints weight = 9752.383| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.65 r_work: 0.3042 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5838 Z= 0.115 Angle : 0.473 4.041 7956 Z= 0.241 Chirality : 0.034 0.122 978 Planarity : 0.004 0.048 976 Dihedral : 5.044 54.165 790 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.58 % Allowed : 15.16 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.09 (0.31), residues: 726 helix: 3.33 (0.20), residues: 602 sheet: None (None), residues: 0 loop : -0.82 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.013 0.002 TYR B 125 PHE 0.015 0.001 PHE B 99 TRP 0.012 0.001 TRP B 394 HIS 0.006 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 5838) covalent geometry : angle 0.47337 ( 7956) hydrogen bonds : bond 0.04332 ( 462) hydrogen bonds : angle 3.56608 ( 1368) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.6239 (tp40) cc_final: 0.5745 (tm-30) REVERT: A 160 TYR cc_start: 0.8900 (t80) cc_final: 0.8531 (t80) REVERT: A 282 GLU cc_start: 0.4464 (mm-30) cc_final: 0.3412 (mm-30) REVERT: B 71 GLN cc_start: 0.6288 (tp40) cc_final: 0.5747 (tm-30) REVERT: B 117 MET cc_start: 0.8210 (mmp) cc_final: 0.8005 (mmt) REVERT: B 282 GLU cc_start: 0.4343 (mm-30) cc_final: 0.3524 (mm-30) outliers start: 16 outliers final: 16 residues processed: 102 average time/residue: 0.1882 time to fit residues: 25.2544 Evaluate side-chains 106 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 46 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 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 = 0.3870 r_free = 0.3870 target = 0.169971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119917 restraints weight = 9791.745| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.67 r_work: 0.3079 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5838 Z= 0.100 Angle : 0.445 4.411 7956 Z= 0.224 Chirality : 0.034 0.122 978 Planarity : 0.004 0.047 976 Dihedral : 4.730 52.480 788 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.94 % Allowed : 15.16 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.43 (0.31), residues: 726 helix: 3.60 (0.20), residues: 594 sheet: None (None), residues: 0 loop : -0.61 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.013 0.002 TYR B 125 PHE 0.010 0.001 PHE B 99 TRP 0.014 0.001 TRP B 394 HIS 0.003 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 5838) covalent geometry : angle 0.44548 ( 7956) hydrogen bonds : bond 0.03799 ( 462) hydrogen bonds : angle 3.37397 ( 1368) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.6214 (tp40) cc_final: 0.5713 (tm-30) REVERT: A 282 GLU cc_start: 0.4554 (mm-30) cc_final: 0.3500 (mm-30) REVERT: B 71 GLN cc_start: 0.6264 (tp40) cc_final: 0.5724 (tm-30) REVERT: B 282 GLU cc_start: 0.4490 (mm-30) cc_final: 0.3428 (mm-30) outliers start: 12 outliers final: 11 residues processed: 98 average time/residue: 0.1747 time to fit residues: 22.3802 Evaluate side-chains 101 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 393 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.166942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.116478 restraints weight = 9773.503| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.67 r_work: 0.3026 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5838 Z= 0.156 Angle : 0.487 4.382 7956 Z= 0.251 Chirality : 0.035 0.123 978 Planarity : 0.004 0.046 976 Dihedral : 4.732 53.526 786 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.94 % Allowed : 15.81 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.24 (0.31), residues: 726 helix: 3.46 (0.20), residues: 596 sheet: None (None), residues: 0 loop : -0.68 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.009 0.002 TYR B 125 PHE 0.014 0.001 PHE A 99 TRP 0.008 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 5838) covalent geometry : angle 0.48691 ( 7956) hydrogen bonds : bond 0.04439 ( 462) hydrogen bonds : angle 3.52048 ( 1368) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.6288 (tp40) cc_final: 0.5749 (tm-30) REVERT: A 160 TYR cc_start: 0.8966 (t80) cc_final: 0.8530 (t80) REVERT: A 282 GLU cc_start: 0.4583 (mm-30) cc_final: 0.3515 (mm-30) REVERT: B 71 GLN cc_start: 0.6321 (tp40) cc_final: 0.5761 (tm-30) REVERT: B 117 MET cc_start: 0.8252 (mmp) cc_final: 0.8022 (mmt) REVERT: B 282 GLU cc_start: 0.4530 (mm-30) cc_final: 0.3492 (mm-30) outliers start: 12 outliers final: 11 residues processed: 100 average time/residue: 0.1853 time to fit residues: 24.2636 Evaluate side-chains 102 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 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 = 0.3849 r_free = 0.3849 target = 0.167870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117645 restraints weight = 9948.520| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.67 r_work: 0.3041 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5838 Z= 0.127 Angle : 0.469 4.579 7956 Z= 0.239 Chirality : 0.034 0.122 978 Planarity : 0.004 0.045 976 Dihedral : 4.622 53.540 784 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.94 % Allowed : 15.97 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.34 (0.31), residues: 726 helix: 3.53 (0.20), residues: 596 sheet: None (None), residues: 0 loop : -0.68 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.011 0.002 TYR B 125 PHE 0.013 0.001 PHE A 99 TRP 0.010 0.001 TRP B 394 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5838) covalent geometry : angle 0.46864 ( 7956) hydrogen bonds : bond 0.04219 ( 462) hydrogen bonds : angle 3.49387 ( 1368) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.6291 (tp40) cc_final: 0.5760 (tm-30) REVERT: A 160 TYR cc_start: 0.8952 (t80) cc_final: 0.8534 (t80) REVERT: A 282 GLU cc_start: 0.4584 (mm-30) cc_final: 0.3510 (mm-30) REVERT: B 71 GLN cc_start: 0.6206 (tp40) cc_final: 0.5681 (tm-30) REVERT: B 282 GLU cc_start: 0.4600 (mm-30) cc_final: 0.3569 (mm-30) outliers start: 12 outliers final: 12 residues processed: 103 average time/residue: 0.1725 time to fit residues: 23.3862 Evaluate side-chains 105 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.170180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.120132 restraints weight = 9951.241| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.68 r_work: 0.3080 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5838 Z= 0.095 Angle : 0.444 4.700 7956 Z= 0.223 Chirality : 0.034 0.123 978 Planarity : 0.004 0.046 976 Dihedral : 4.496 52.638 784 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.61 % Allowed : 16.45 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.64 (0.31), residues: 726 helix: 3.75 (0.20), residues: 596 sheet: None (None), residues: 0 loop : -0.62 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 370 TYR 0.012 0.002 TYR B 125 PHE 0.009 0.001 PHE B 99 TRP 0.014 0.001 TRP B 394 HIS 0.002 0.000 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 5838) covalent geometry : angle 0.44450 ( 7956) hydrogen bonds : bond 0.03711 ( 462) hydrogen bonds : angle 3.35443 ( 1368) =============================================================================== Job complete usr+sys time: 3073.07 seconds wall clock time: 52 minutes 50.45 seconds (3170.45 seconds total)