Starting phenix.real_space_refine on Tue Mar 3 14:19:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rtn_24684/03_2026/7rtn_24684.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtn_24684/03_2026/7rtn_24684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rtn_24684/03_2026/7rtn_24684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtn_24684/03_2026/7rtn_24684.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rtn_24684/03_2026/7rtn_24684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtn_24684/03_2026/7rtn_24684.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 3792 2.51 5 N 1098 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 6018 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 9, 'PHE:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 9, 'PHE:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 9, 'PHE:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 92 Time building chain proxies: 1.57, per 1000 atoms: 0.26 Number of scatterers: 6018 At special positions: 0 Unit cell: (104.72, 104.72, 111.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1116 8.00 N 1098 7.00 C 3792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 378.1 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 56.7% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.967A pdb=" N SER A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 135 removed outlier: 3.719A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 340 Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.982A pdb=" N VAL A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 446 through 455 removed outlier: 3.911A pdb=" N ARG A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 484 through 491 Processing helix chain 'A' and resid 494 through 508 Processing helix chain 'B' and resid 65 through 79 removed outlier: 4.009A pdb=" N LYS B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 135 removed outlier: 3.531A pdb=" N ARG B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 135 " --> pdb=" O TYR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 340 removed outlier: 3.970A pdb=" N GLY B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.755A pdb=" N PHE B 354 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS B 355 " --> pdb=" O MET B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 438 removed outlier: 3.550A pdb=" N SER B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 455 removed outlier: 3.953A pdb=" N THR B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 483 through 491 Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'C' and resid 65 through 79 Processing helix chain 'C' and resid 89 through 135 removed outlier: 3.501A pdb=" N ARG C 93 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 340 Proline residue: C 326 - end of helix removed outlier: 4.037A pdb=" N GLY C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 424 through 438 Processing helix chain 'C' and resid 445 through 454 Processing helix chain 'C' and resid 469 through 483 removed outlier: 3.843A pdb=" N VAL C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 491 removed outlier: 3.838A pdb=" N HIS C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.586A pdb=" N ARG C 500 " --> pdb=" O HIS C 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 406 removed outlier: 5.696A pdb=" N ILE A 364 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER A 463 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A 366 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 414 Processing sheet with id=AA3, first strand: chain 'B' and resid 401 through 408 removed outlier: 6.666A pdb=" N ILE B 364 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER B 463 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL B 366 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 410 through 414 Processing sheet with id=AA5, first strand: chain 'C' and resid 401 through 406 removed outlier: 6.421A pdb=" N ILE C 364 " --> pdb=" O SER C 463 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER C 463 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL C 366 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 410 through 414 408 hydrogen bonds defined for protein. 1176 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: 0.61 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2085 1.34 - 1.46: 1019 1.46 - 1.58: 3022 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 6144 Sorted by residual: bond pdb=" CG LYS B 98 " pdb=" CD LYS B 98 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CA GLN C 444 " pdb=" CB GLN C 444 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.08e+00 bond pdb=" CB GLU C 82 " pdb=" CG GLU C 82 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.31e-01 bond pdb=" CG GLU C 82 " pdb=" CD GLU C 82 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.25e-01 bond pdb=" N GLN C 444 " pdb=" CA GLN C 444 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 7.98e-01 ... (remaining 6139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 8200 2.00 - 3.99: 123 3.99 - 5.99: 11 5.99 - 7.99: 7 7.99 - 9.99: 2 Bond angle restraints: 8343 Sorted by residual: angle pdb=" C THR C 443 " pdb=" N GLN C 444 " pdb=" CA GLN C 444 " ideal model delta sigma weight residual 121.54 129.05 -7.51 1.91e+00 2.74e-01 1.55e+01 angle pdb=" C THR B 443 " pdb=" N GLN B 444 " pdb=" CA GLN B 444 " ideal model delta sigma weight residual 121.54 128.76 -7.22 1.91e+00 2.74e-01 1.43e+01 angle pdb=" C HIS C 384 " pdb=" N HIS C 385 " pdb=" CA HIS C 385 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" CA LEU B 414 " pdb=" CB LEU B 414 " pdb=" CG LEU B 414 " ideal model delta sigma weight residual 116.30 126.29 -9.99 3.50e+00 8.16e-02 8.14e+00 angle pdb=" CA GLN C 444 " pdb=" CB GLN C 444 " pdb=" CG GLN C 444 " ideal model delta sigma weight residual 114.10 119.53 -5.43 2.00e+00 2.50e-01 7.36e+00 ... (remaining 8338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3244 17.84 - 35.68: 311 35.68 - 53.52: 55 53.52 - 71.36: 10 71.36 - 89.19: 4 Dihedral angle restraints: 3624 sinusoidal: 1284 harmonic: 2340 Sorted by residual: dihedral pdb=" CA TYR C 65 " pdb=" C TYR C 65 " pdb=" N GLY C 66 " pdb=" CA GLY C 66 " ideal model delta harmonic sigma weight residual 180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA HIS B 385 " pdb=" C HIS B 385 " pdb=" N HIS B 386 " pdb=" CA HIS B 386 " ideal model delta harmonic sigma weight residual 180.00 158.93 21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA HIS A 385 " pdb=" C HIS A 385 " pdb=" N HIS A 386 " pdb=" CA HIS A 386 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 3621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 584 0.035 - 0.070: 249 0.070 - 0.105: 70 0.105 - 0.139: 25 0.139 - 0.174: 2 Chirality restraints: 930 Sorted by residual: chirality pdb=" CB ILE B 399 " pdb=" CA ILE B 399 " pdb=" CG1 ILE B 399 " pdb=" CG2 ILE B 399 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA PRO A 370 " pdb=" N PRO A 370 " pdb=" C PRO A 370 " pdb=" CB PRO A 370 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CG LEU C 433 " pdb=" CB LEU C 433 " pdb=" CD1 LEU C 433 " pdb=" CD2 LEU C 433 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 927 not shown) Planarity restraints: 1107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 89 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO C 90 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 89 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO A 90 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 378 " -0.013 2.00e-02 2.50e+03 9.35e-03 1.53e+00 pdb=" CG PHE C 378 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE C 378 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 378 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 378 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 378 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 378 " -0.005 2.00e-02 2.50e+03 ... (remaining 1104 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1748 2.82 - 3.34: 5705 3.34 - 3.86: 9613 3.86 - 4.38: 10615 4.38 - 4.90: 18932 Nonbonded interactions: 46613 Sorted by model distance: nonbonded pdb=" O ALA B 369 " pdb=" OG SER B 373 " model vdw 2.298 3.040 nonbonded pdb=" O HIS A 384 " pdb=" ND1 HIS A 385 " model vdw 2.311 3.120 nonbonded pdb=" O HIS B 384 " pdb=" ND1 HIS B 385 " model vdw 2.317 3.120 nonbonded pdb=" O SER C 89 " pdb=" OG SER C 89 " model vdw 2.351 3.040 nonbonded pdb=" OD2 ASP C 86 " pdb=" NH2 ARG C 499 " model vdw 2.353 3.120 ... (remaining 46608 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' selection = chain 'B' selection = chain 'C' } 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: 1.530 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.770 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6144 Z= 0.157 Angle : 0.631 9.986 8343 Z= 0.333 Chirality : 0.044 0.174 930 Planarity : 0.004 0.036 1107 Dihedral : 14.578 89.195 2112 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 0.60 (0.31), residues: 798 helix: 1.96 (0.25), residues: 423 sheet: -0.01 (0.44), residues: 139 loop : -2.36 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 93 TYR 0.015 0.001 TYR A 367 PHE 0.020 0.002 PHE C 378 TRP 0.017 0.002 TRP A 371 HIS 0.008 0.001 HIS B 489 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6144) covalent geometry : angle 0.63069 ( 8343) hydrogen bonds : bond 0.10663 ( 408) hydrogen bonds : angle 5.16068 ( 1176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.230 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0706 time to fit residues: 11.0481 Evaluate side-chains 86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.172549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145758 restraints weight = 9696.717| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.26 r_work: 0.3515 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6144 Z= 0.157 Angle : 0.584 8.409 8343 Z= 0.311 Chirality : 0.042 0.156 930 Planarity : 0.004 0.035 1107 Dihedral : 4.492 21.398 870 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.80 % Allowed : 10.81 % Favored : 87.39 % 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: 0.72 (0.31), residues: 798 helix: 2.09 (0.25), residues: 436 sheet: -0.11 (0.44), residues: 142 loop : -2.56 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 500 TYR 0.014 0.001 TYR A 367 PHE 0.019 0.002 PHE A 378 TRP 0.016 0.002 TRP A 371 HIS 0.006 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6144) covalent geometry : angle 0.58432 ( 8343) hydrogen bonds : bond 0.04231 ( 408) hydrogen bonds : angle 4.35571 ( 1176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.220 Fit side-chains REVERT: B 92 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7925 (mt-10) REVERT: B 482 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7304 (p90) outliers start: 10 outliers final: 7 residues processed: 90 average time/residue: 0.0689 time to fit residues: 8.5606 Evaluate side-chains 90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 63 optimal weight: 50.0000 chunk 33 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 58 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.172214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145268 restraints weight = 9551.072| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.40 r_work: 0.3513 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6144 Z= 0.135 Angle : 0.548 8.570 8343 Z= 0.290 Chirality : 0.041 0.143 930 Planarity : 0.004 0.035 1107 Dihedral : 4.314 21.064 870 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.88 % Allowed : 12.07 % Favored : 85.05 % 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: 0.88 (0.31), residues: 798 helix: 2.26 (0.25), residues: 433 sheet: 0.11 (0.45), residues: 136 loop : -2.57 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 500 TYR 0.016 0.001 TYR C 482 PHE 0.018 0.002 PHE A 378 TRP 0.014 0.001 TRP A 371 HIS 0.007 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6144) covalent geometry : angle 0.54834 ( 8343) hydrogen bonds : bond 0.03946 ( 408) hydrogen bonds : angle 4.19292 ( 1176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.189 Fit side-chains REVERT: A 438 SER cc_start: 0.8259 (m) cc_final: 0.7916 (p) REVERT: B 92 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7979 (mt-10) REVERT: B 482 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7167 (p90) REVERT: B 489 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8281 (m-70) outliers start: 16 outliers final: 12 residues processed: 99 average time/residue: 0.0590 time to fit residues: 8.1706 Evaluate side-chains 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 27 optimal weight: 40.0000 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 34 optimal weight: 0.0070 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.171902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145218 restraints weight = 9724.513| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.30 r_work: 0.3522 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6144 Z= 0.141 Angle : 0.548 8.284 8343 Z= 0.291 Chirality : 0.041 0.137 930 Planarity : 0.004 0.035 1107 Dihedral : 4.311 21.141 870 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.42 % Allowed : 13.87 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.89 (0.31), residues: 798 helix: 2.27 (0.25), residues: 433 sheet: 0.11 (0.45), residues: 136 loop : -2.56 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 500 TYR 0.016 0.001 TYR A 466 PHE 0.018 0.002 PHE A 378 TRP 0.015 0.002 TRP A 371 HIS 0.008 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6144) covalent geometry : angle 0.54848 ( 8343) hydrogen bonds : bond 0.03950 ( 408) hydrogen bonds : angle 4.15953 ( 1176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.235 Fit side-chains REVERT: A 438 SER cc_start: 0.8402 (m) cc_final: 0.8038 (p) REVERT: B 92 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8117 (mt-10) REVERT: B 482 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7257 (p90) REVERT: B 489 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.8374 (m170) outliers start: 19 outliers final: 14 residues processed: 96 average time/residue: 0.0637 time to fit residues: 8.5677 Evaluate side-chains 99 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 3 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 chunk 4 optimal weight: 40.0000 chunk 15 optimal weight: 0.2980 chunk 41 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.172147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145888 restraints weight = 9813.987| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.16 r_work: 0.3549 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6144 Z= 0.144 Angle : 0.554 8.206 8343 Z= 0.294 Chirality : 0.041 0.147 930 Planarity : 0.004 0.035 1107 Dihedral : 4.321 21.073 870 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.14 % Allowed : 14.41 % Favored : 81.44 % 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: 0.93 (0.31), residues: 798 helix: 2.30 (0.25), residues: 431 sheet: 0.13 (0.45), residues: 136 loop : -2.51 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 500 TYR 0.011 0.001 TYR A 367 PHE 0.019 0.002 PHE A 378 TRP 0.012 0.002 TRP A 371 HIS 0.009 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6144) covalent geometry : angle 0.55384 ( 8343) hydrogen bonds : bond 0.03952 ( 408) hydrogen bonds : angle 4.14377 ( 1176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.159 Fit side-chains REVERT: A 438 SER cc_start: 0.8207 (m) cc_final: 0.7862 (p) REVERT: B 92 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7885 (mt-10) REVERT: B 105 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: B 482 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.7110 (p90) REVERT: B 489 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.8310 (m-70) outliers start: 23 outliers final: 16 residues processed: 103 average time/residue: 0.0557 time to fit residues: 8.2253 Evaluate side-chains 98 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 73 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 37 optimal weight: 40.0000 overall best weight: 5.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.173183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146606 restraints weight = 9670.210| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.15 r_work: 0.3563 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6144 Z= 0.139 Angle : 0.553 8.004 8343 Z= 0.293 Chirality : 0.041 0.139 930 Planarity : 0.003 0.035 1107 Dihedral : 4.286 20.889 870 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.78 % Allowed : 15.32 % Favored : 80.90 % 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: 0.98 (0.31), residues: 798 helix: 2.34 (0.25), residues: 431 sheet: 0.30 (0.46), residues: 133 loop : -2.55 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.017 0.001 TYR A 466 PHE 0.018 0.002 PHE C 378 TRP 0.015 0.002 TRP A 371 HIS 0.009 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6144) covalent geometry : angle 0.55325 ( 8343) hydrogen bonds : bond 0.03884 ( 408) hydrogen bonds : angle 4.11007 ( 1176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.199 Fit side-chains REVERT: A 438 SER cc_start: 0.8364 (m) cc_final: 0.8006 (p) REVERT: B 92 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8100 (mt-10) REVERT: B 105 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: B 482 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7268 (p90) REVERT: B 489 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8266 (m-70) outliers start: 21 outliers final: 18 residues processed: 99 average time/residue: 0.0565 time to fit residues: 8.0431 Evaluate side-chains 104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 33 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.172211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.147648 restraints weight = 9644.219| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.09 r_work: 0.3522 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6144 Z= 0.160 Angle : 0.572 8.073 8343 Z= 0.303 Chirality : 0.042 0.135 930 Planarity : 0.004 0.034 1107 Dihedral : 4.447 21.245 870 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.50 % Allowed : 15.32 % Favored : 80.18 % 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: 0.94 (0.31), residues: 798 helix: 2.28 (0.25), residues: 431 sheet: 0.17 (0.45), residues: 139 loop : -2.49 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.012 0.001 TYR A 367 PHE 0.019 0.002 PHE A 378 TRP 0.016 0.002 TRP A 371 HIS 0.010 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6144) covalent geometry : angle 0.57222 ( 8343) hydrogen bonds : bond 0.04084 ( 408) hydrogen bonds : angle 4.18013 ( 1176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.214 Fit side-chains REVERT: A 115 TYR cc_start: 0.2538 (OUTLIER) cc_final: 0.2275 (t80) REVERT: A 385 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7007 (p-80) REVERT: B 92 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8140 (mt-10) REVERT: B 105 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: B 482 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7268 (p90) REVERT: B 489 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8281 (m-70) REVERT: C 103 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6515 (tm-30) outliers start: 25 outliers final: 17 residues processed: 102 average time/residue: 0.0600 time to fit residues: 8.8795 Evaluate side-chains 103 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 50 optimal weight: 8.9990 chunk 22 optimal weight: 0.0020 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 42 optimal weight: 0.2980 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 overall best weight: 3.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 HIS B 457 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.174320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.148186 restraints weight = 9653.704| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.25 r_work: 0.3534 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6144 Z= 0.110 Angle : 0.528 7.908 8343 Z= 0.278 Chirality : 0.040 0.140 930 Planarity : 0.003 0.033 1107 Dihedral : 4.076 20.179 870 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.78 % Allowed : 15.50 % Favored : 80.72 % 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: 1.22 (0.31), residues: 798 helix: 2.51 (0.25), residues: 432 sheet: 0.82 (0.48), residues: 124 loop : -2.57 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.017 0.001 TYR A 466 PHE 0.019 0.002 PHE C 392 TRP 0.017 0.001 TRP A 371 HIS 0.008 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 6144) covalent geometry : angle 0.52756 ( 8343) hydrogen bonds : bond 0.03544 ( 408) hydrogen bonds : angle 3.95429 ( 1176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.259 Fit side-chains REVERT: A 115 TYR cc_start: 0.2262 (OUTLIER) cc_final: 0.1994 (t80) REVERT: A 438 SER cc_start: 0.8214 (m) cc_final: 0.7872 (p) REVERT: B 105 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: B 445 MET cc_start: 0.8443 (ttt) cc_final: 0.8218 (ttt) REVERT: B 482 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.6773 (p90) REVERT: B 489 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8268 (m-70) outliers start: 21 outliers final: 16 residues processed: 97 average time/residue: 0.0612 time to fit residues: 8.4283 Evaluate side-chains 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 67 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 40.0000 chunk 62 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.171994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145627 restraints weight = 9704.950| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.21 r_work: 0.3497 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6144 Z= 0.154 Angle : 0.570 8.071 8343 Z= 0.302 Chirality : 0.042 0.144 930 Planarity : 0.004 0.031 1107 Dihedral : 4.361 21.598 870 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.32 % Allowed : 15.86 % Favored : 79.82 % 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: 1.05 (0.31), residues: 798 helix: 2.36 (0.25), residues: 432 sheet: 0.24 (0.45), residues: 139 loop : -2.47 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.017 0.001 TYR A 466 PHE 0.018 0.002 PHE A 378 TRP 0.016 0.002 TRP A 371 HIS 0.010 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6144) covalent geometry : angle 0.57040 ( 8343) hydrogen bonds : bond 0.03949 ( 408) hydrogen bonds : angle 4.10126 ( 1176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.162 Fit side-chains REVERT: A 115 TYR cc_start: 0.2767 (OUTLIER) cc_final: 0.2271 (t80) REVERT: A 385 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7105 (p-80) REVERT: A 438 SER cc_start: 0.8288 (m) cc_final: 0.7942 (p) REVERT: B 92 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8056 (mt-10) REVERT: B 105 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: B 482 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7245 (p90) REVERT: B 489 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.8297 (m-70) outliers start: 24 outliers final: 17 residues processed: 101 average time/residue: 0.0550 time to fit residues: 7.9702 Evaluate side-chains 100 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 34 optimal weight: 50.0000 chunk 8 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.172215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146119 restraints weight = 9680.857| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.16 r_work: 0.3524 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6144 Z= 0.147 Angle : 0.557 7.382 8343 Z= 0.297 Chirality : 0.041 0.156 930 Planarity : 0.004 0.031 1107 Dihedral : 4.359 22.721 870 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.96 % Allowed : 16.04 % Favored : 80.00 % 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: 1.01 (0.31), residues: 798 helix: 2.34 (0.25), residues: 432 sheet: 0.15 (0.44), residues: 144 loop : -2.51 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.015 0.001 TYR A 466 PHE 0.018 0.002 PHE C 378 TRP 0.017 0.002 TRP A 371 HIS 0.010 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6144) covalent geometry : angle 0.55712 ( 8343) hydrogen bonds : bond 0.03889 ( 408) hydrogen bonds : angle 4.09820 ( 1176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.236 Fit side-chains REVERT: A 115 TYR cc_start: 0.2832 (OUTLIER) cc_final: 0.2245 (t80) REVERT: A 385 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7037 (p-80) REVERT: A 438 SER cc_start: 0.8288 (m) cc_final: 0.7943 (p) REVERT: B 92 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8019 (mt-10) REVERT: B 105 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: B 482 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7268 (p90) REVERT: B 489 HIS cc_start: 0.8541 (OUTLIER) cc_final: 0.8279 (m-70) outliers start: 22 outliers final: 17 residues processed: 97 average time/residue: 0.0606 time to fit residues: 8.4540 Evaluate side-chains 103 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 72 optimal weight: 5.9990 chunk 7 optimal weight: 40.0000 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.171819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145641 restraints weight = 9634.703| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.14 r_work: 0.3505 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6144 Z= 0.154 Angle : 0.564 7.404 8343 Z= 0.301 Chirality : 0.042 0.166 930 Planarity : 0.004 0.031 1107 Dihedral : 4.410 24.863 870 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.14 % Allowed : 16.04 % Favored : 79.82 % 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: 0.99 (0.31), residues: 798 helix: 2.30 (0.25), residues: 432 sheet: 0.14 (0.44), residues: 144 loop : -2.47 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.015 0.001 TYR A 466 PHE 0.018 0.002 PHE C 378 TRP 0.016 0.002 TRP A 371 HIS 0.010 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6144) covalent geometry : angle 0.56361 ( 8343) hydrogen bonds : bond 0.03968 ( 408) hydrogen bonds : angle 4.12596 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1642.51 seconds wall clock time: 28 minutes 41.16 seconds (1721.16 seconds total)