Starting phenix.real_space_refine on Sat Aug 23 07:37:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gso_34237/08_2025/8gso_34237_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gso_34237/08_2025/8gso_34237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gso_34237/08_2025/8gso_34237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gso_34237/08_2025/8gso_34237.map" model { file = "/net/cci-nas-00/data/ceres_data/8gso_34237/08_2025/8gso_34237_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gso_34237/08_2025/8gso_34237_neut.cif" } resolution = 3.3 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= -0.001 sd= 0.031 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 36 5.16 5 C 7060 2.51 5 N 1700 2.21 5 O 1828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10624 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5312 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 30, 'TRANS': 630} Chain breaks: 1 Chain: "B" Number of atoms: 5312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5312 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 30, 'TRANS': 630} Chain breaks: 1 Time building chain proxies: 2.63, per 1000 atoms: 0.25 Number of scatterers: 10624 At special positions: 0 Unit cell: (119.262, 112.59, 100.914, 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 36 16.00 O 1828 8.00 N 1700 7.00 C 7060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 418.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 71.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 80 through 110 Proline residue: A 104 - end of helix Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.536A pdb=" N ASN A 136 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 183 removed outlier: 4.529A pdb=" N VAL A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.044A pdb=" N GLU A 232 " --> pdb=" O VAL A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.732A pdb=" N ASN A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 348 through 353 removed outlier: 4.368A pdb=" N ASN A 353 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 389 Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.628A pdb=" N GLN A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 395' Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.589A pdb=" N MET A 428 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 444 through 484 removed outlier: 4.020A pdb=" N LYS A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 483 " --> pdb=" O LYS A 479 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 523 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 523 through 537 removed outlier: 4.428A pdb=" N LYS A 535 " --> pdb=" O HIS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.583A pdb=" N VAL A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 582 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 612 through 638 removed outlier: 4.234A pdb=" N LEU A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 646 through 665 removed outlier: 3.796A pdb=" N LEU A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 689 through 693 removed outlier: 3.555A pdb=" N TYR A 693 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 28 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 80 through 110 Proline residue: B 104 - end of helix Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.536A pdb=" N ASN B 136 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 183 removed outlier: 4.529A pdb=" N VAL B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 229 through 232 removed outlier: 4.044A pdb=" N GLU B 232 " --> pdb=" O VAL B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.732A pdb=" N ASN B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 304 Processing helix chain 'B' and resid 317 through 326 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 4.368A pdb=" N ASN B 353 " --> pdb=" O GLN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 389 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 416 through 438 removed outlier: 3.589A pdb=" N MET B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 444 through 477 Processing helix chain 'B' and resid 489 through 523 Proline residue: B 499 - end of helix Processing helix chain 'B' and resid 523 through 537 removed outlier: 4.428A pdb=" N LYS B 535 " --> pdb=" O HIS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.583A pdb=" N VAL B 544 " --> pdb=" O THR B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 582 through 594 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 612 through 638 removed outlier: 4.234A pdb=" N LEU B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 646 through 665 removed outlier: 3.796A pdb=" N LEU B 654 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 689 through 693 removed outlier: 3.555A pdb=" N TYR B 693 " --> pdb=" O PHE B 690 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1544 1.27 - 1.40: 2908 1.40 - 1.54: 6299 1.54 - 1.68: 95 1.68 - 1.81: 60 Bond restraints: 10906 Sorted by residual: bond pdb=" C PHE A 95 " pdb=" O PHE A 95 " ideal model delta sigma weight residual 1.236 1.133 0.103 1.16e-02 7.43e+03 7.93e+01 bond pdb=" C PHE B 95 " pdb=" O PHE B 95 " ideal model delta sigma weight residual 1.236 1.133 0.103 1.16e-02 7.43e+03 7.93e+01 bond pdb=" C THR B 496 " pdb=" O THR B 496 " ideal model delta sigma weight residual 1.236 1.323 -0.087 1.16e-02 7.43e+03 5.68e+01 bond pdb=" C THR A 496 " pdb=" O THR A 496 " ideal model delta sigma weight residual 1.236 1.323 -0.087 1.16e-02 7.43e+03 5.68e+01 bond pdb=" N THR B 389 " pdb=" CA THR B 389 " ideal model delta sigma weight residual 1.463 1.559 -0.096 1.30e-02 5.92e+03 5.51e+01 ... (remaining 10901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 13746 2.93 - 5.87: 878 5.87 - 8.80: 149 8.80 - 11.74: 41 11.74 - 14.67: 10 Bond angle restraints: 14824 Sorted by residual: angle pdb=" C LEU A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta sigma weight residual 119.56 108.73 10.83 1.02e+00 9.61e-01 1.13e+02 angle pdb=" C LEU B 107 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " ideal model delta sigma weight residual 119.56 108.73 10.83 1.02e+00 9.61e-01 1.13e+02 angle pdb=" N LYS B 145 " pdb=" CA LYS B 145 " pdb=" C LYS B 145 " ideal model delta sigma weight residual 109.96 95.29 14.67 1.49e+00 4.50e-01 9.69e+01 angle pdb=" N LYS A 145 " pdb=" CA LYS A 145 " pdb=" C LYS A 145 " ideal model delta sigma weight residual 109.96 95.29 14.67 1.49e+00 4.50e-01 9.69e+01 angle pdb=" N PHE B 632 " pdb=" CA PHE B 632 " pdb=" C PHE B 632 " ideal model delta sigma weight residual 113.88 101.88 12.00 1.23e+00 6.61e-01 9.51e+01 ... (remaining 14819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4960 17.46 - 34.91: 716 34.91 - 52.37: 485 52.37 - 69.82: 251 69.82 - 87.28: 22 Dihedral angle restraints: 6434 sinusoidal: 2526 harmonic: 3908 Sorted by residual: dihedral pdb=" C ILE B 397 " pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" CB ILE B 397 " ideal model delta harmonic sigma weight residual -122.00 -136.17 14.17 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" C ILE B 379 " pdb=" N ILE B 379 " pdb=" CA ILE B 379 " pdb=" CB ILE B 379 " ideal model delta harmonic sigma weight residual -122.00 -135.10 13.10 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" C ILE A 379 " pdb=" N ILE A 379 " pdb=" CA ILE A 379 " pdb=" CB ILE A 379 " ideal model delta harmonic sigma weight residual -122.00 -135.10 13.10 0 2.50e+00 1.60e-01 2.75e+01 ... (remaining 6431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1305 0.111 - 0.221: 324 0.221 - 0.332: 57 0.332 - 0.442: 26 0.442 - 0.553: 10 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA PRO B 499 " pdb=" N PRO B 499 " pdb=" C PRO B 499 " pdb=" CB PRO B 499 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA PRO A 499 " pdb=" N PRO A 499 " pdb=" C PRO A 499 " pdb=" CB PRO A 499 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA ILE B 397 " pdb=" N ILE B 397 " pdb=" C ILE B 397 " pdb=" CB ILE B 397 " both_signs ideal model delta sigma weight residual False 2.43 1.91 0.52 2.00e-01 2.50e+01 6.74e+00 ... (remaining 1719 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 107 " 0.123 5.00e-02 4.00e+02 1.85e-01 5.50e+01 pdb=" N PRO A 108 " -0.321 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.106 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 107 " -0.123 5.00e-02 4.00e+02 1.85e-01 5.50e+01 pdb=" N PRO B 108 " 0.321 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " -0.106 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 498 " 0.121 5.00e-02 4.00e+02 1.81e-01 5.25e+01 pdb=" N PRO A 499 " -0.313 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " 0.105 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 20 1.93 - 2.68: 842 2.68 - 3.42: 15677 3.42 - 4.16: 27139 4.16 - 4.90: 46532 Nonbonded interactions: 90210 Sorted by model distance: nonbonded pdb=" CZ2 TRP A 240 " pdb=" CE LYS A 294 " model vdw 1.194 3.740 nonbonded pdb=" CZ2 TRP B 240 " pdb=" CE LYS B 294 " model vdw 1.194 3.740 nonbonded pdb=" NE1 TRP A 240 " pdb=" NZ LYS A 294 " model vdw 1.407 3.200 nonbonded pdb=" NE1 TRP B 240 " pdb=" NZ LYS B 294 " model vdw 1.407 3.200 nonbonded pdb=" CE2 TRP B 240 " pdb=" NZ LYS B 294 " model vdw 1.446 3.340 ... (remaining 90205 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.180 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 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 : 0.013 0.103 10906 Z= 0.963 Angle : 1.663 14.670 14824 Z= 1.143 Chirality : 0.112 0.553 1722 Planarity : 0.014 0.185 1808 Dihedral : 25.120 87.276 3902 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 6.70 % Allowed : 17.05 % Favored : 76.26 % Rotamer: Outliers : 41.49 % Allowed : 12.07 % Favored : 46.44 % Cbeta Deviations : 1.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.21 (0.18), residues: 1314 helix: -2.57 (0.13), residues: 864 sheet: -6.27 (0.42), residues: 24 loop : -4.97 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 226 TYR 0.010 0.002 TYR B 555 PHE 0.030 0.002 PHE B 513 TRP 0.022 0.002 TRP A 548 HIS 0.005 0.001 HIS B 617 Details of bonding type rmsd covalent geometry : bond 0.01263 (10906) covalent geometry : angle 1.66307 (14824) hydrogen bonds : bond 0.17560 ( 633) hydrogen bonds : angle 8.36204 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 478 poor density : 314 time to evaluate : 0.424 Fit side-chains REVERT: A 2 GLU cc_start: 0.4885 (OUTLIER) cc_final: 0.4439 (tt0) REVERT: A 104 PRO cc_start: 0.6399 (OUTLIER) cc_final: 0.5087 (Cg_exo) REVERT: A 120 LYS cc_start: 0.5868 (OUTLIER) cc_final: 0.5664 (mmmt) REVERT: A 169 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7412 (tttm) REVERT: A 204 ASP cc_start: -0.0318 (OUTLIER) cc_final: -0.0536 (t0) REVERT: A 223 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7772 (p) REVERT: A 337 THR cc_start: 0.7627 (m) cc_final: 0.7148 (p) REVERT: A 420 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8096 (mt) REVERT: A 466 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7251 (mp) REVERT: A 481 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8489 (tt) REVERT: A 532 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8004 (mt) REVERT: A 607 GLU cc_start: 0.7583 (tp30) cc_final: 0.7127 (mm-30) REVERT: A 619 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8112 (mmt90) REVERT: B 2 GLU cc_start: 0.4908 (OUTLIER) cc_final: 0.4550 (tt0) REVERT: B 104 PRO cc_start: 0.6415 (OUTLIER) cc_final: 0.5093 (Cg_exo) REVERT: B 169 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7415 (tttm) REVERT: B 204 ASP cc_start: -0.0315 (OUTLIER) cc_final: -0.0536 (t0) REVERT: B 223 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7776 (p) REVERT: B 337 THR cc_start: 0.7632 (m) cc_final: 0.7150 (p) REVERT: B 420 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8114 (mt) REVERT: B 466 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7244 (mp) REVERT: B 532 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7998 (mt) REVERT: B 607 GLU cc_start: 0.7579 (tp30) cc_final: 0.7124 (mm-30) REVERT: B 619 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8107 (mmt90) outliers start: 478 outliers final: 87 residues processed: 634 average time/residue: 0.1173 time to fit residues: 101.9112 Evaluate side-chains 299 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 192 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 PRO Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 499 PRO Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 PRO Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 PRO Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 660 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 136 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN A 596 ASN A 617 HIS A 628 GLN B 40 ASN B 136 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN B 596 ASN B 628 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.160575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125328 restraints weight = 13414.119| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.33 r_work: 0.3346 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10906 Z= 0.225 Angle : 0.915 9.650 14824 Z= 0.478 Chirality : 0.051 0.244 1722 Planarity : 0.008 0.083 1808 Dihedral : 13.110 65.381 1635 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 1.29 % Allowed : 13.55 % Favored : 85.16 % Rotamer: Outliers : 10.68 % Allowed : 23.70 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.92 (0.22), residues: 1314 helix: -0.59 (0.16), residues: 898 sheet: -6.29 (0.40), residues: 24 loop : -4.87 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 395 TYR 0.013 0.002 TYR B 572 PHE 0.024 0.002 PHE B 369 TRP 0.023 0.003 TRP B 49 HIS 0.003 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00498 (10906) covalent geometry : angle 0.91539 (14824) hydrogen bonds : bond 0.06593 ( 633) hydrogen bonds : angle 5.34250 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 199 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: A 63 ARG cc_start: 0.7853 (mtm110) cc_final: 0.7535 (ttp80) REVERT: A 120 LYS cc_start: 0.6304 (OUTLIER) cc_final: 0.5609 (mmmt) REVERT: A 141 ASN cc_start: 0.5329 (t0) cc_final: 0.4931 (t0) REVERT: A 334 ASP cc_start: 0.8036 (t0) cc_final: 0.7722 (t0) REVERT: A 337 THR cc_start: 0.9060 (m) cc_final: 0.8483 (p) REVERT: A 376 PHE cc_start: 0.7809 (m-10) cc_final: 0.7082 (t80) REVERT: B 47 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: B 59 PHE cc_start: 0.8568 (m-10) cc_final: 0.8358 (m-10) REVERT: B 141 ASN cc_start: 0.5320 (t0) cc_final: 0.4920 (t0) REVERT: B 334 ASP cc_start: 0.8039 (t0) cc_final: 0.7724 (t0) REVERT: B 337 THR cc_start: 0.9055 (m) cc_final: 0.8486 (p) REVERT: B 376 PHE cc_start: 0.7797 (m-10) cc_final: 0.7081 (t80) outliers start: 123 outliers final: 53 residues processed: 301 average time/residue: 0.0786 time to fit residues: 36.8486 Evaluate side-chains 206 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 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 115 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.156206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121509 restraints weight = 13564.492| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.31 r_work: 0.3300 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10906 Z= 0.189 Angle : 0.784 8.876 14824 Z= 0.406 Chirality : 0.047 0.186 1722 Planarity : 0.006 0.073 1808 Dihedral : 10.085 71.659 1501 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.68 % Allowed : 13.62 % Favored : 85.69 % Rotamer: Outliers : 7.90 % Allowed : 26.13 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.23), residues: 1314 helix: 0.22 (0.17), residues: 892 sheet: -4.64 (1.17), residues: 10 loop : -4.49 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 678 TYR 0.011 0.001 TYR B 164 PHE 0.021 0.002 PHE B 513 TRP 0.018 0.002 TRP A 49 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00425 (10906) covalent geometry : angle 0.78435 (14824) hydrogen bonds : bond 0.05692 ( 633) hydrogen bonds : angle 5.01121 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 182 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: A 72 ASP cc_start: 0.8513 (m-30) cc_final: 0.8091 (t0) REVERT: A 351 ASN cc_start: 0.8040 (p0) cc_final: 0.7794 (p0) REVERT: A 376 PHE cc_start: 0.7898 (m-10) cc_final: 0.6910 (t80) REVERT: A 478 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8234 (m) REVERT: A 489 MET cc_start: 0.5058 (OUTLIER) cc_final: 0.4839 (ptt) REVERT: A 521 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8666 (tt) REVERT: A 573 SER cc_start: 0.9375 (t) cc_final: 0.8930 (m) REVERT: B 47 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: B 63 ARG cc_start: 0.7815 (mtm110) cc_final: 0.7524 (ttp80) REVERT: B 72 ASP cc_start: 0.8513 (m-30) cc_final: 0.8093 (t0) REVERT: B 141 ASN cc_start: 0.5728 (t0) cc_final: 0.5501 (t0) REVERT: B 351 ASN cc_start: 0.8055 (p0) cc_final: 0.7812 (p0) REVERT: B 376 PHE cc_start: 0.7911 (m-10) cc_final: 0.6909 (t80) REVERT: B 521 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8665 (tt) REVERT: B 573 SER cc_start: 0.9360 (t) cc_final: 0.8920 (m) outliers start: 91 outliers final: 55 residues processed: 257 average time/residue: 0.0810 time to fit residues: 32.1927 Evaluate side-chains 229 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 106 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.0270 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN A 628 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120257 restraints weight = 13579.752| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.28 r_work: 0.3283 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10906 Z= 0.169 Angle : 0.738 9.587 14824 Z= 0.382 Chirality : 0.045 0.196 1722 Planarity : 0.006 0.062 1808 Dihedral : 9.111 74.944 1489 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.68 % Allowed : 12.48 % Favored : 86.83 % Rotamer: Outliers : 6.34 % Allowed : 28.39 % Favored : 65.28 % 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 aren not related in a simple way. whole: -1.36 (0.24), residues: 1314 helix: 0.59 (0.18), residues: 878 sheet: -4.62 (1.15), residues: 10 loop : -4.18 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 678 TYR 0.008 0.001 TYR B 456 PHE 0.021 0.001 PHE A 513 TRP 0.019 0.002 TRP A 548 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00379 (10906) covalent geometry : angle 0.73773 (14824) hydrogen bonds : bond 0.05223 ( 633) hydrogen bonds : angle 4.98140 ( 1851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 177 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: A 63 ARG cc_start: 0.7832 (mtm110) cc_final: 0.7564 (ttp80) REVERT: A 72 ASP cc_start: 0.8496 (m-30) cc_final: 0.8077 (t0) REVERT: A 198 ASP cc_start: 0.8242 (t0) cc_final: 0.8028 (t0) REVERT: A 332 MET cc_start: 0.7544 (ppp) cc_final: 0.7119 (ppp) REVERT: A 351 ASN cc_start: 0.8119 (p0) cc_final: 0.7855 (p0) REVERT: A 376 PHE cc_start: 0.7873 (m-10) cc_final: 0.6686 (t80) REVERT: A 390 LEU cc_start: 0.7846 (tp) cc_final: 0.7608 (tp) REVERT: A 475 PHE cc_start: 0.7865 (m-10) cc_final: 0.7607 (m-10) REVERT: A 478 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8154 (m) REVERT: A 489 MET cc_start: 0.4970 (OUTLIER) cc_final: 0.4630 (ptt) REVERT: A 573 SER cc_start: 0.9282 (t) cc_final: 0.8918 (m) REVERT: A 611 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8031 (tpt-90) REVERT: B 47 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: B 63 ARG cc_start: 0.7804 (mtm110) cc_final: 0.7535 (ttp80) REVERT: B 72 ASP cc_start: 0.8494 (m-30) cc_final: 0.8077 (t0) REVERT: B 136 ASN cc_start: 0.8191 (t0) cc_final: 0.7531 (t0) REVERT: B 141 ASN cc_start: 0.5736 (t0) cc_final: 0.5403 (t0) REVERT: B 198 ASP cc_start: 0.8221 (t0) cc_final: 0.8006 (t0) REVERT: B 332 MET cc_start: 0.7547 (ppp) cc_final: 0.7124 (ppp) REVERT: B 351 ASN cc_start: 0.8085 (p0) cc_final: 0.7829 (p0) REVERT: B 376 PHE cc_start: 0.7883 (m-10) cc_final: 0.6688 (t80) REVERT: B 573 SER cc_start: 0.9275 (t) cc_final: 0.8917 (m) REVERT: B 611 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8027 (tpt-90) outliers start: 73 outliers final: 44 residues processed: 234 average time/residue: 0.0857 time to fit residues: 30.5965 Evaluate side-chains 208 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117426 restraints weight = 13477.400| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.28 r_work: 0.3260 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10906 Z= 0.176 Angle : 0.740 9.775 14824 Z= 0.379 Chirality : 0.045 0.198 1722 Planarity : 0.006 0.059 1808 Dihedral : 8.169 79.390 1473 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.40 % Favored : 87.14 % Rotamer: Outliers : 7.20 % Allowed : 27.78 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.24), residues: 1314 helix: 0.76 (0.18), residues: 884 sheet: -5.13 (0.80), residues: 20 loop : -3.84 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 678 TYR 0.006 0.001 TYR A 171 PHE 0.022 0.001 PHE B 513 TRP 0.018 0.002 TRP B 548 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00409 (10906) covalent geometry : angle 0.74012 (14824) hydrogen bonds : bond 0.05137 ( 633) hydrogen bonds : angle 4.97699 ( 1851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 163 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7952 (mtm110) cc_final: 0.7645 (ttp80) REVERT: A 72 ASP cc_start: 0.8542 (m-30) cc_final: 0.8170 (t0) REVERT: A 107 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7829 (mp) REVERT: A 136 ASN cc_start: 0.8689 (t0) cc_final: 0.8450 (t0) REVERT: A 332 MET cc_start: 0.7764 (ppp) cc_final: 0.7338 (ppp) REVERT: A 334 ASP cc_start: 0.7777 (t0) cc_final: 0.7552 (t0) REVERT: A 376 PHE cc_start: 0.7933 (m-10) cc_final: 0.6856 (t80) REVERT: A 390 LEU cc_start: 0.8051 (tp) cc_final: 0.7824 (tp) REVERT: A 478 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8368 (m) REVERT: A 573 SER cc_start: 0.9116 (t) cc_final: 0.8808 (m) REVERT: A 611 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8301 (tpt-90) REVERT: B 63 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7623 (ttp80) REVERT: B 72 ASP cc_start: 0.8544 (m-30) cc_final: 0.8175 (t0) REVERT: B 107 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7832 (mp) REVERT: B 136 ASN cc_start: 0.8645 (t0) cc_final: 0.8420 (t0) REVERT: B 141 ASN cc_start: 0.5546 (t0) cc_final: 0.5162 (t0) REVERT: B 332 MET cc_start: 0.7775 (ppp) cc_final: 0.7348 (ppp) REVERT: B 334 ASP cc_start: 0.7783 (t0) cc_final: 0.7556 (t0) REVERT: B 376 PHE cc_start: 0.7910 (m-10) cc_final: 0.6838 (t80) REVERT: B 501 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8407 (p) REVERT: B 573 SER cc_start: 0.9124 (t) cc_final: 0.8809 (m) REVERT: B 611 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8316 (tpt-90) outliers start: 83 outliers final: 50 residues processed: 226 average time/residue: 0.0805 time to fit residues: 27.6494 Evaluate side-chains 196 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 140 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 26 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112682 restraints weight = 13583.774| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.35 r_work: 0.3180 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10906 Z= 0.188 Angle : 0.733 8.176 14824 Z= 0.380 Chirality : 0.045 0.181 1722 Planarity : 0.005 0.057 1808 Dihedral : 7.955 86.618 1463 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.40 % Favored : 87.06 % Rotamer: Outliers : 7.47 % Allowed : 26.91 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.24), residues: 1314 helix: 0.72 (0.17), residues: 904 sheet: None (None), residues: 0 loop : -3.80 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 318 TYR 0.007 0.001 TYR B 364 PHE 0.023 0.002 PHE A 513 TRP 0.027 0.002 TRP A 548 HIS 0.004 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00437 (10906) covalent geometry : angle 0.73281 (14824) hydrogen bonds : bond 0.05180 ( 633) hydrogen bonds : angle 5.01011 ( 1851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 168 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7991 (tt) REVERT: A 63 ARG cc_start: 0.7798 (mtm110) cc_final: 0.7526 (ttp80) REVERT: A 72 ASP cc_start: 0.8444 (m-30) cc_final: 0.8019 (t0) REVERT: A 107 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7716 (mp) REVERT: A 332 MET cc_start: 0.7841 (ppp) cc_final: 0.7410 (ppp) REVERT: A 376 PHE cc_start: 0.7869 (m-10) cc_final: 0.6580 (t80) REVERT: A 478 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8061 (m) REVERT: A 573 SER cc_start: 0.9369 (t) cc_final: 0.8940 (m) REVERT: A 611 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8294 (tpt-90) REVERT: B 46 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7981 (tt) REVERT: B 63 ARG cc_start: 0.7738 (mtm110) cc_final: 0.7468 (ttp80) REVERT: B 72 ASP cc_start: 0.8453 (m-30) cc_final: 0.8027 (t0) REVERT: B 107 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7744 (mp) REVERT: B 141 ASN cc_start: 0.5656 (t0) cc_final: 0.5408 (t0) REVERT: B 332 MET cc_start: 0.7814 (ppp) cc_final: 0.7390 (ppp) REVERT: B 376 PHE cc_start: 0.7836 (m-10) cc_final: 0.6612 (t80) REVERT: B 501 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8262 (p) REVERT: B 573 SER cc_start: 0.9364 (t) cc_final: 0.8924 (m) REVERT: B 611 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8299 (tpt-90) outliers start: 86 outliers final: 48 residues processed: 228 average time/residue: 0.0861 time to fit residues: 29.0468 Evaluate side-chains 194 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 138 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114763 restraints weight = 13547.221| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.35 r_work: 0.3212 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10906 Z= 0.162 Angle : 0.718 8.274 14824 Z= 0.371 Chirality : 0.045 0.200 1722 Planarity : 0.005 0.056 1808 Dihedral : 7.315 59.940 1456 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.02 % Favored : 87.44 % Rotamer: Outliers : 6.86 % Allowed : 27.60 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.24), residues: 1314 helix: 0.87 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -3.67 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 318 TYR 0.006 0.001 TYR B 364 PHE 0.020 0.001 PHE B 513 TRP 0.033 0.002 TRP B 548 HIS 0.004 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00369 (10906) covalent geometry : angle 0.71815 (14824) hydrogen bonds : bond 0.04960 ( 633) hydrogen bonds : angle 4.95682 ( 1851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 158 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7791 (mtm110) cc_final: 0.7529 (ttp80) REVERT: A 72 ASP cc_start: 0.8310 (m-30) cc_final: 0.7929 (t0) REVERT: A 107 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 332 MET cc_start: 0.7711 (ppp) cc_final: 0.7228 (ppp) REVERT: A 335 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7990 (mmtp) REVERT: A 376 PHE cc_start: 0.7868 (m-10) cc_final: 0.6611 (t80) REVERT: A 478 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.8020 (m) REVERT: A 573 SER cc_start: 0.9308 (t) cc_final: 0.8885 (m) REVERT: A 611 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8338 (tpt-90) REVERT: B 63 ARG cc_start: 0.7779 (mtm110) cc_final: 0.7518 (ttp80) REVERT: B 72 ASP cc_start: 0.8316 (m-30) cc_final: 0.7938 (t0) REVERT: B 107 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7655 (mp) REVERT: B 199 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8925 (ptm) REVERT: B 332 MET cc_start: 0.7694 (ppp) cc_final: 0.7216 (ppp) REVERT: B 335 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.7972 (mmtp) REVERT: B 376 PHE cc_start: 0.7843 (m-10) cc_final: 0.6608 (t80) REVERT: B 501 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8154 (p) REVERT: B 573 SER cc_start: 0.9333 (t) cc_final: 0.8913 (m) REVERT: B 611 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8343 (tpt-90) outliers start: 79 outliers final: 53 residues processed: 211 average time/residue: 0.0859 time to fit residues: 27.1404 Evaluate side-chains 214 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 152 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113744 restraints weight = 13574.348| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.36 r_work: 0.3197 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10906 Z= 0.168 Angle : 0.737 10.390 14824 Z= 0.377 Chirality : 0.046 0.250 1722 Planarity : 0.006 0.055 1808 Dihedral : 6.911 59.964 1452 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.48 % Favored : 86.99 % Rotamer: Outliers : 6.16 % Allowed : 28.73 % Favored : 65.10 % 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 aren not related in a simple way. whole: -0.54 (0.24), residues: 1314 helix: 0.98 (0.18), residues: 902 sheet: None (None), residues: 0 loop : -3.56 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 318 TYR 0.007 0.001 TYR B 364 PHE 0.022 0.001 PHE A 513 TRP 0.031 0.002 TRP B 548 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00387 (10906) covalent geometry : angle 0.73704 (14824) hydrogen bonds : bond 0.04941 ( 633) hydrogen bonds : angle 4.95106 ( 1851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 156 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7805 (mtm110) cc_final: 0.7534 (ttp80) REVERT: A 72 ASP cc_start: 0.8332 (m-30) cc_final: 0.7966 (t0) REVERT: A 107 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7623 (mp) REVERT: A 198 ASP cc_start: 0.8149 (t0) cc_final: 0.7619 (t0) REVERT: A 332 MET cc_start: 0.7837 (ppp) cc_final: 0.7394 (ppp) REVERT: A 334 ASP cc_start: 0.7592 (t0) cc_final: 0.7155 (t0) REVERT: A 335 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8027 (mmtp) REVERT: A 376 PHE cc_start: 0.7882 (m-10) cc_final: 0.6665 (t80) REVERT: A 478 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8056 (m) REVERT: A 573 SER cc_start: 0.9328 (t) cc_final: 0.8908 (m) REVERT: A 611 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8383 (tpt-90) REVERT: B 63 ARG cc_start: 0.7783 (mtm110) cc_final: 0.7515 (ttp80) REVERT: B 72 ASP cc_start: 0.8343 (m-30) cc_final: 0.7979 (t0) REVERT: B 107 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7609 (mp) REVERT: B 198 ASP cc_start: 0.8270 (t0) cc_final: 0.7889 (t0) REVERT: B 332 MET cc_start: 0.7825 (ppp) cc_final: 0.7386 (ppp) REVERT: B 334 ASP cc_start: 0.7553 (t0) cc_final: 0.7061 (t0) REVERT: B 335 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8003 (mmtp) REVERT: B 376 PHE cc_start: 0.7890 (m-10) cc_final: 0.6660 (t80) REVERT: B 573 SER cc_start: 0.9318 (t) cc_final: 0.8901 (m) REVERT: B 611 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8385 (tpt-90) outliers start: 71 outliers final: 50 residues processed: 207 average time/residue: 0.0925 time to fit residues: 28.0647 Evaluate side-chains 203 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 146 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.0670 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 55 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118222 restraints weight = 13371.760| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.36 r_work: 0.3260 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.7107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10906 Z= 0.148 Angle : 0.710 9.767 14824 Z= 0.363 Chirality : 0.045 0.213 1722 Planarity : 0.005 0.053 1808 Dihedral : 6.500 57.708 1448 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.18 % Favored : 87.29 % Rotamer: Outliers : 5.03 % Allowed : 28.99 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.24), residues: 1314 helix: 1.11 (0.18), residues: 906 sheet: None (None), residues: 0 loop : -3.65 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 395 TYR 0.007 0.001 TYR B 517 PHE 0.017 0.001 PHE B 513 TRP 0.029 0.002 TRP B 548 HIS 0.004 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00327 (10906) covalent geometry : angle 0.71027 (14824) hydrogen bonds : bond 0.04581 ( 633) hydrogen bonds : angle 4.85280 ( 1851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 177 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7625 (ttp80) REVERT: A 72 ASP cc_start: 0.8317 (m-30) cc_final: 0.7967 (t0) REVERT: A 107 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7454 (mp) REVERT: A 198 ASP cc_start: 0.8209 (t0) cc_final: 0.7743 (t0) REVERT: A 332 MET cc_start: 0.7817 (ppp) cc_final: 0.7442 (ppp) REVERT: A 334 ASP cc_start: 0.7423 (t0) cc_final: 0.7034 (t0) REVERT: A 335 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7941 (mmtp) REVERT: A 376 PHE cc_start: 0.7865 (m-10) cc_final: 0.6628 (t80) REVERT: A 478 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8074 (m) REVERT: A 573 SER cc_start: 0.9256 (t) cc_final: 0.8845 (m) REVERT: B 63 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7580 (ttp80) REVERT: B 72 ASP cc_start: 0.8328 (m-30) cc_final: 0.7982 (t0) REVERT: B 107 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7506 (mp) REVERT: B 332 MET cc_start: 0.7800 (ppp) cc_final: 0.7423 (ppp) REVERT: B 335 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.7960 (mmtp) REVERT: B 376 PHE cc_start: 0.7871 (m-10) cc_final: 0.6654 (t80) REVERT: B 501 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.8098 (p) REVERT: B 573 SER cc_start: 0.9251 (t) cc_final: 0.8840 (m) outliers start: 58 outliers final: 43 residues processed: 219 average time/residue: 0.0879 time to fit residues: 28.6691 Evaluate side-chains 202 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.0070 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 0.0770 chunk 90 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120676 restraints weight = 13401.996| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.30 r_work: 0.3303 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.7256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10906 Z= 0.148 Angle : 0.706 9.994 14824 Z= 0.361 Chirality : 0.044 0.209 1722 Planarity : 0.005 0.051 1808 Dihedral : 6.243 57.803 1445 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.33 % Favored : 87.29 % Rotamer: Outliers : 3.91 % Allowed : 29.95 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.25), residues: 1314 helix: 1.09 (0.18), residues: 918 sheet: None (None), residues: 0 loop : -3.60 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 395 TYR 0.012 0.001 TYR A 536 PHE 0.018 0.001 PHE B 513 TRP 0.028 0.002 TRP B 548 HIS 0.004 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00324 (10906) covalent geometry : angle 0.70558 (14824) hydrogen bonds : bond 0.04498 ( 633) hydrogen bonds : angle 4.83561 ( 1851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7725 (ttp80) REVERT: A 72 ASP cc_start: 0.8397 (m-30) cc_final: 0.8106 (t0) REVERT: A 107 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7612 (mp) REVERT: A 198 ASP cc_start: 0.8230 (t0) cc_final: 0.7771 (t0) REVERT: A 332 MET cc_start: 0.7832 (ppp) cc_final: 0.7576 (ppp) REVERT: A 334 ASP cc_start: 0.7403 (t0) cc_final: 0.6994 (t0) REVERT: A 335 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8068 (mmtp) REVERT: A 376 PHE cc_start: 0.7929 (m-10) cc_final: 0.6805 (t80) REVERT: A 478 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8201 (m) REVERT: A 573 SER cc_start: 0.9077 (t) cc_final: 0.8750 (m) REVERT: B 63 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7682 (ttp80) REVERT: B 72 ASP cc_start: 0.8383 (m-30) cc_final: 0.8087 (t0) REVERT: B 107 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7610 (mp) REVERT: B 332 MET cc_start: 0.7840 (ppp) cc_final: 0.7581 (ppp) REVERT: B 335 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8045 (mmtp) REVERT: B 376 PHE cc_start: 0.7939 (m-10) cc_final: 0.6815 (t80) REVERT: B 573 SER cc_start: 0.9086 (t) cc_final: 0.8755 (m) outliers start: 45 outliers final: 37 residues processed: 196 average time/residue: 0.0763 time to fit residues: 23.0474 Evaluate side-chains 201 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 79 optimal weight: 0.0060 chunk 24 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 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 = 0.3770 r_free = 0.3770 target = 0.151547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115636 restraints weight = 13598.462| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.34 r_work: 0.3233 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.7308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10906 Z= 0.165 Angle : 0.717 9.777 14824 Z= 0.368 Chirality : 0.045 0.198 1722 Planarity : 0.005 0.049 1808 Dihedral : 6.255 58.969 1445 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.33 % Favored : 87.29 % Rotamer: Outliers : 4.17 % Allowed : 29.17 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.25), residues: 1314 helix: 1.10 (0.18), residues: 916 sheet: None (None), residues: 0 loop : -3.54 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 395 TYR 0.011 0.001 TYR B 536 PHE 0.023 0.001 PHE B 513 TRP 0.024 0.002 TRP B 548 HIS 0.005 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00381 (10906) covalent geometry : angle 0.71714 (14824) hydrogen bonds : bond 0.04715 ( 633) hydrogen bonds : angle 4.86657 ( 1851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2819.40 seconds wall clock time: 49 minutes 4.62 seconds (2944.62 seconds total)