Starting phenix.real_space_refine on Sat Aug 23 07:37:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gro_34210/08_2025/8gro_34210_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gro_34210/08_2025/8gro_34210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gro_34210/08_2025/8gro_34210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gro_34210/08_2025/8gro_34210.map" model { file = "/net/cci-nas-00/data/ceres_data/8gro_34210/08_2025/8gro_34210_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gro_34210/08_2025/8gro_34210_neut.cif" } resolution = 3.5 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= 0.024 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: 1.91, per 1000 atoms: 0.18 Number of scatterers: 10624 At special positions: 0 Unit cell: (114.258, 114.258, 103.416, 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: 0.90 Conformation dependent library (CDL) restraints added in 373.9 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 71.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 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 389 through 396 removed outlier: 4.069A pdb=" N ILE A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.588A 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 482 removed outlier: 3.824A pdb=" N LYS A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A 480 " --> pdb=" O ASN A 476 " (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: 3.795A 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: 3.556A 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 389 through 397 removed outlier: 4.428A pdb=" N ILE B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 416 through 438 removed outlier: 3.588A 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 480 removed outlier: 3.941A pdb=" N LYS B 479 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) 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: 3.795A 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: 3.556A pdb=" N TYR B 693 " --> pdb=" O PHE B 690 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1872 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: 1.35 Time building geometry restraints manager: 1.13 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: 1542 1.27 - 1.40: 2908 1.40 - 1.54: 6311 1.54 - 1.68: 85 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 1.132 0.104 1.16e-02 7.43e+03 7.97e+01 bond pdb=" C PHE B 95 " pdb=" O PHE B 95 " ideal model delta sigma weight residual 1.236 1.132 0.104 1.16e-02 7.43e+03 7.97e+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 5.58e+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 5.58e+01 bond pdb=" N THR A 389 " pdb=" CA THR A 389 " ideal model delta sigma weight residual 1.463 1.559 -0.096 1.30e-02 5.92e+03 5.50e+01 ... (remaining 10901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 13733 2.93 - 5.87: 887 5.87 - 8.80: 154 8.80 - 11.74: 42 11.74 - 14.67: 8 Bond angle restraints: 14824 Sorted by residual: angle pdb=" C LEU B 107 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " ideal model delta sigma weight residual 119.56 108.71 10.85 1.02e+00 9.61e-01 1.13e+02 angle pdb=" C LEU A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta sigma weight residual 119.56 108.71 10.85 1.02e+00 9.61e-01 1.13e+02 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 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 PHE B 632 " pdb=" CA PHE B 632 " pdb=" C PHE B 632 " ideal model delta sigma weight residual 113.88 101.90 11.98 1.23e+00 6.61e-01 9.49e+01 ... (remaining 14819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4945 17.46 - 34.92: 726 34.92 - 52.38: 482 52.38 - 69.84: 259 69.84 - 87.30: 22 Dihedral angle restraints: 6434 sinusoidal: 2526 harmonic: 3908 Sorted by residual: 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 -135.13 13.13 0 2.50e+00 1.60e-01 2.76e+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 -135.13 13.13 0 2.50e+00 1.60e-01 2.76e+01 dihedral pdb=" C VAL A 559 " pdb=" N VAL A 559 " pdb=" CA VAL A 559 " pdb=" CB VAL A 559 " ideal model delta harmonic sigma weight residual -122.00 -134.25 12.25 0 2.50e+00 1.60e-01 2.40e+01 ... (remaining 6431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1301 0.110 - 0.220: 325 0.220 - 0.330: 62 0.330 - 0.440: 26 0.440 - 0.550: 8 Chirality restraints: 1722 Sorted by residual: 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 7.57e+00 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 7.57e+00 chirality pdb=" CA LEU B 103 " pdb=" N LEU B 103 " pdb=" C LEU B 103 " pdb=" CB LEU B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.18e+00 ... (remaining 1719 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 107 " -0.123 5.00e-02 4.00e+02 1.86e-01 5.51e+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 107 " 0.123 5.00e-02 4.00e+02 1.86e-01 5.51e+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 498 " 0.121 5.00e-02 4.00e+02 1.81e-01 5.26e+01 pdb=" N PRO B 499 " -0.313 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " 0.105 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.94: 10 1.94 - 2.68: 835 2.68 - 3.42: 15682 3.42 - 4.16: 27148 4.16 - 4.90: 46423 Nonbonded interactions: 90098 Sorted by model distance: nonbonded pdb=" CZ2 TRP B 240 " pdb=" CE LYS B 294 " model vdw 1.194 3.740 nonbonded pdb=" CZ2 TRP A 240 " pdb=" CE LYS A 294 " model vdw 1.194 3.740 nonbonded pdb=" NE1 TRP B 240 " pdb=" NZ LYS B 294 " model vdw 1.408 3.200 nonbonded pdb=" NE1 TRP A 240 " pdb=" NZ LYS A 294 " model vdw 1.408 3.200 nonbonded pdb=" CE2 TRP A 240 " pdb=" NZ LYS A 294 " model vdw 1.446 3.340 ... (remaining 90093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.900 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 0.104 10906 Z= 0.964 Angle : 1.667 14.669 14824 Z= 1.149 Chirality : 0.111 0.550 1722 Planarity : 0.014 0.186 1808 Dihedral : 25.245 87.304 3902 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 6.62 % Allowed : 16.29 % Favored : 77.09 % Rotamer: Outliers : 41.49 % Allowed : 13.11 % Favored : 45.40 % Cbeta Deviations : 1.34 % 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: -2.60 (0.13), residues: 876 sheet: -6.27 (0.42), residues: 24 loop : -4.95 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 226 TYR 0.010 0.002 TYR B 555 PHE 0.030 0.002 PHE A 513 TRP 0.022 0.002 TRP A 548 HIS 0.005 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.01264 (10906) covalent geometry : angle 1.66685 (14824) hydrogen bonds : bond 0.17115 ( 640) hydrogen bonds : angle 8.32837 ( 1872) *********************** 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 777 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 478 poor density : 299 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5703 (tt0) REVERT: A 104 PRO cc_start: 0.7192 (OUTLIER) cc_final: 0.5730 (Cg_exo) REVERT: A 144 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6699 (mtmm) REVERT: A 153 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7634 (tp) REVERT: A 187 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8193 (t) REVERT: A 229 VAL cc_start: 0.6806 (OUTLIER) cc_final: 0.6550 (t) REVERT: A 236 VAL cc_start: 0.4525 (OUTLIER) cc_final: 0.4252 (t) REVERT: A 287 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.4398 (mp) REVERT: A 363 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6279 (mt0) REVERT: A 466 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.6823 (mt) REVERT: A 492 ASN cc_start: 0.3974 (OUTLIER) cc_final: 0.3700 (t0) REVERT: A 513 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6231 (t80) REVERT: A 545 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7328 (mmtm) REVERT: A 595 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6946 (ttt90) REVERT: A 641 PHE cc_start: 0.4896 (OUTLIER) cc_final: 0.4302 (m-10) REVERT: A 680 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7580 (mt) REVERT: B 2 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5779 (tt0) REVERT: B 104 PRO cc_start: 0.7174 (OUTLIER) cc_final: 0.5705 (Cg_exo) REVERT: B 144 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6685 (mtmm) REVERT: B 187 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8180 (t) REVERT: B 229 VAL cc_start: 0.6785 (OUTLIER) cc_final: 0.6536 (t) REVERT: B 236 VAL cc_start: 0.4539 (OUTLIER) cc_final: 0.4251 (t) REVERT: B 287 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.4380 (mp) REVERT: B 363 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6329 (mt0) REVERT: B 400 ILE cc_start: 0.6313 (OUTLIER) cc_final: 0.6060 (tt) REVERT: B 466 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.6825 (mt) REVERT: B 492 ASN cc_start: 0.4013 (OUTLIER) cc_final: 0.3710 (t0) REVERT: B 499 PRO cc_start: 0.8688 (OUTLIER) cc_final: 0.8478 (Cg_exo) REVERT: B 513 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6214 (t80) REVERT: B 545 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7323 (mmtm) REVERT: B 595 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6967 (ttt90) REVERT: B 641 PHE cc_start: 0.4862 (OUTLIER) cc_final: 0.4295 (m-10) REVERT: B 680 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7571 (mt) outliers start: 478 outliers final: 120 residues processed: 642 average time/residue: 0.0944 time to fit residues: 83.2992 Evaluate side-chains 337 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 184 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 104 PRO Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 ASP 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 144 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 411 THR 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 484 ASN Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 104 PRO Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 ASP 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 144 LYS Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 411 THR 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 478 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 499 PRO Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 680 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 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 33 ASN A 40 ASN A 75 ASN A 208 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 HIS A 628 GLN A 662 GLN B 33 ASN B 40 ASN B 75 ASN B 208 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 HIS B 628 GLN B 662 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.140817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.111043 restraints weight = 17759.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.114691 restraints weight = 7298.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.116960 restraints weight = 4541.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117660 restraints weight = 3558.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.118438 restraints weight = 3254.255| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10906 Z= 0.218 Angle : 0.913 12.283 14824 Z= 0.478 Chirality : 0.049 0.210 1722 Planarity : 0.007 0.088 1808 Dihedral : 14.979 81.940 1743 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.91 % Allowed : 13.55 % Favored : 85.54 % Rotamer: Outliers : 12.67 % Allowed : 24.48 % Favored : 62.85 % 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: -3.09 (0.22), residues: 1314 helix: -0.78 (0.16), residues: 896 sheet: -6.61 (0.27), residues: 24 loop : -4.73 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 395 TYR 0.019 0.002 TYR B 215 PHE 0.020 0.002 PHE B 224 TRP 0.021 0.002 TRP A 613 HIS 0.008 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00466 (10906) covalent geometry : angle 0.91285 (14824) hydrogen bonds : bond 0.06812 ( 640) hydrogen bonds : angle 5.33465 ( 1872) *********************** 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 382 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 236 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5972 (tmm) cc_final: 0.5513 (tmm) REVERT: A 103 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7028 (mp) REVERT: A 171 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.8809 (t80) REVERT: A 229 VAL cc_start: 0.7637 (OUTLIER) cc_final: 0.7383 (t) REVERT: A 236 VAL cc_start: 0.6758 (OUTLIER) cc_final: 0.5417 (t) REVERT: A 339 THR cc_start: 0.8884 (t) cc_final: 0.8654 (t) REVERT: A 459 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7491 (t80) REVERT: A 487 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 581 ILE cc_start: 0.9037 (tt) cc_final: 0.8822 (tt) REVERT: A 679 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7687 (pm20) REVERT: A 682 GLN cc_start: 0.8301 (mt0) cc_final: 0.8091 (pp30) REVERT: A 690 PHE cc_start: 0.8027 (t80) cc_final: 0.7673 (t80) REVERT: B 21 MET cc_start: 0.5975 (tmm) cc_final: 0.5518 (tmm) REVERT: B 103 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7032 (mp) REVERT: B 171 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.8803 (t80) REVERT: B 229 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7387 (t) REVERT: B 236 VAL cc_start: 0.6764 (OUTLIER) cc_final: 0.5430 (t) REVERT: B 339 THR cc_start: 0.8880 (t) cc_final: 0.8649 (t) REVERT: B 459 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7480 (t80) REVERT: B 492 ASN cc_start: 0.5732 (OUTLIER) cc_final: 0.5529 (t0) REVERT: B 505 PHE cc_start: 0.8284 (m-80) cc_final: 0.8050 (m-80) REVERT: B 581 ILE cc_start: 0.9038 (tt) cc_final: 0.8825 (tt) REVERT: B 679 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7687 (pm20) REVERT: B 682 GLN cc_start: 0.8315 (mt0) cc_final: 0.8089 (pp30) REVERT: B 690 PHE cc_start: 0.8027 (t80) cc_final: 0.7673 (t80) outliers start: 146 outliers final: 72 residues processed: 337 average time/residue: 0.0893 time to fit residues: 45.1987 Evaluate side-chains 266 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 182 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 125 THR 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 183 MET Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 134 LEU 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 183 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.111526 restraints weight = 17899.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.115065 restraints weight = 7396.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.117271 restraints weight = 4570.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.118294 restraints weight = 3564.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118674 restraints weight = 3187.965| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10906 Z= 0.183 Angle : 0.792 8.880 14824 Z= 0.411 Chirality : 0.046 0.218 1722 Planarity : 0.006 0.079 1808 Dihedral : 11.279 57.914 1532 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.68 % Allowed : 12.79 % Favored : 86.53 % Rotamer: Outliers : 9.03 % Allowed : 27.00 % Favored : 63.98 % 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: -2.10 (0.23), residues: 1314 helix: -0.05 (0.17), residues: 898 sheet: -6.46 (0.33), residues: 24 loop : -4.28 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 395 TYR 0.016 0.001 TYR B 572 PHE 0.019 0.001 PHE A 224 TRP 0.019 0.002 TRP A 613 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00392 (10906) covalent geometry : angle 0.79246 (14824) hydrogen bonds : bond 0.05785 ( 640) hydrogen bonds : angle 5.10868 ( 1872) *********************** 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 315 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 211 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8534 (t80) REVERT: A 236 VAL cc_start: 0.6223 (OUTLIER) cc_final: 0.4994 (t) REVERT: A 339 THR cc_start: 0.8912 (t) cc_final: 0.8703 (t) REVERT: A 385 SER cc_start: 0.8591 (t) cc_final: 0.8208 (p) REVERT: A 431 LYS cc_start: 0.8043 (tmtt) cc_final: 0.7477 (mptt) REVERT: A 581 ILE cc_start: 0.9065 (tt) cc_final: 0.8806 (tt) REVERT: A 612 MET cc_start: 0.8704 (tpt) cc_final: 0.8461 (tpt) REVERT: A 641 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5548 (m-80) REVERT: A 686 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 690 PHE cc_start: 0.8035 (t80) cc_final: 0.7714 (t80) REVERT: B 171 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8529 (t80) REVERT: B 236 VAL cc_start: 0.6239 (OUTLIER) cc_final: 0.5005 (t) REVERT: B 339 THR cc_start: 0.8910 (t) cc_final: 0.8701 (t) REVERT: B 385 SER cc_start: 0.8507 (t) cc_final: 0.8091 (p) REVERT: B 431 LYS cc_start: 0.8050 (tmtt) cc_final: 0.7482 (mptt) REVERT: B 581 ILE cc_start: 0.9069 (tt) cc_final: 0.8799 (tt) REVERT: B 612 MET cc_start: 0.8704 (tpt) cc_final: 0.8459 (tpt) REVERT: B 641 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5526 (m-80) REVERT: B 686 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8602 (tp) REVERT: B 690 PHE cc_start: 0.8032 (t80) cc_final: 0.7709 (t80) outliers start: 104 outliers final: 59 residues processed: 286 average time/residue: 0.0863 time to fit residues: 36.9895 Evaluate side-chains 246 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 179 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 125 THR 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 183 MET Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 491 ILE 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 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 134 LEU 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 183 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 487 LEU 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 563 MET Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 106 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 HIS A 670 HIS A 682 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 ASN B 531 HIS B 662 GLN B 670 HIS B 682 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.134960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.106473 restraints weight = 17579.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.109889 restraints weight = 7297.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111988 restraints weight = 4416.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113292 restraints weight = 3399.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113667 restraints weight = 2945.590| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10906 Z= 0.194 Angle : 0.787 10.323 14824 Z= 0.406 Chirality : 0.046 0.217 1722 Planarity : 0.006 0.075 1808 Dihedral : 10.151 59.237 1502 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.95 % Favored : 87.60 % Rotamer: Outliers : 8.68 % Allowed : 26.82 % Favored : 64.50 % 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: -1.72 (0.24), residues: 1314 helix: 0.19 (0.17), residues: 910 sheet: -6.30 (0.28), residues: 34 loop : -4.03 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 197 TYR 0.014 0.001 TYR A 572 PHE 0.018 0.001 PHE B 513 TRP 0.016 0.002 TRP A 613 HIS 0.002 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00436 (10906) covalent geometry : angle 0.78724 (14824) hydrogen bonds : bond 0.05630 ( 640) hydrogen bonds : angle 5.02139 ( 1872) *********************** 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 301 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 201 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8580 (p) REVERT: A 171 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.8409 (t80) REVERT: A 190 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8369 (pp20) REVERT: A 210 GLU cc_start: 0.9100 (mp0) cc_final: 0.8771 (mp0) REVERT: A 236 VAL cc_start: 0.6390 (OUTLIER) cc_final: 0.5999 (m) REVERT: A 328 LEU cc_start: 0.8822 (tp) cc_final: 0.8615 (tt) REVERT: A 339 THR cc_start: 0.8883 (t) cc_final: 0.8660 (t) REVERT: A 385 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8127 (p) REVERT: A 496 THR cc_start: 0.8640 (m) cc_final: 0.8377 (p) REVERT: A 563 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7968 (mtt) REVERT: A 581 ILE cc_start: 0.9070 (tt) cc_final: 0.8782 (tt) REVERT: A 624 LEU cc_start: 0.8904 (tm) cc_final: 0.8669 (tm) REVERT: A 641 PHE cc_start: 0.6001 (OUTLIER) cc_final: 0.5425 (m-80) REVERT: A 686 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8470 (tp) REVERT: A 690 PHE cc_start: 0.8139 (t80) cc_final: 0.7758 (t80) REVERT: B 69 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8588 (p) REVERT: B 171 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.8402 (t80) REVERT: B 190 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8367 (pp20) REVERT: B 210 GLU cc_start: 0.9105 (mp0) cc_final: 0.8774 (mp0) REVERT: B 236 VAL cc_start: 0.6404 (OUTLIER) cc_final: 0.6013 (m) REVERT: B 328 LEU cc_start: 0.8815 (tp) cc_final: 0.8612 (tt) REVERT: B 339 THR cc_start: 0.8876 (t) cc_final: 0.8651 (t) REVERT: B 385 SER cc_start: 0.8402 (t) cc_final: 0.7917 (p) REVERT: B 496 THR cc_start: 0.8664 (m) cc_final: 0.8425 (p) REVERT: B 563 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8012 (mtt) REVERT: B 581 ILE cc_start: 0.9069 (tt) cc_final: 0.8783 (tt) REVERT: B 624 LEU cc_start: 0.8913 (tm) cc_final: 0.8677 (tm) REVERT: B 641 PHE cc_start: 0.6024 (OUTLIER) cc_final: 0.5448 (m-80) REVERT: B 686 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8465 (tp) REVERT: B 690 PHE cc_start: 0.8145 (t80) cc_final: 0.7765 (t80) outliers start: 100 outliers final: 52 residues processed: 277 average time/residue: 0.0844 time to fit residues: 35.3999 Evaluate side-chains 247 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 180 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 ASN 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 153 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 134 LEU 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 183 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 0.0000 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 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 = 0.3858 r_free = 0.3858 target = 0.138029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.109918 restraints weight = 17427.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113306 restraints weight = 7259.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115446 restraints weight = 4432.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116371 restraints weight = 3408.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117221 restraints weight = 3028.674| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10906 Z= 0.168 Angle : 0.769 8.790 14824 Z= 0.393 Chirality : 0.046 0.221 1722 Planarity : 0.006 0.070 1808 Dihedral : 9.506 58.924 1495 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.80 % Favored : 87.75 % Rotamer: Outliers : 7.99 % Allowed : 27.43 % Favored : 64.58 % 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: -1.23 (0.24), residues: 1314 helix: 0.45 (0.17), residues: 920 sheet: -5.68 (0.53), residues: 20 loop : -3.83 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 197 TYR 0.019 0.001 TYR B 215 PHE 0.022 0.001 PHE A 224 TRP 0.017 0.002 TRP A 240 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00367 (10906) covalent geometry : angle 0.76893 (14824) hydrogen bonds : bond 0.05312 ( 640) hydrogen bonds : angle 4.98784 ( 1872) *********************** 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 272 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 180 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8362 (t80) REVERT: A 210 GLU cc_start: 0.9063 (mp0) cc_final: 0.8817 (mp0) REVERT: A 236 VAL cc_start: 0.6556 (OUTLIER) cc_final: 0.6200 (m) REVERT: A 328 LEU cc_start: 0.8844 (tp) cc_final: 0.8611 (tt) REVERT: A 339 THR cc_start: 0.8902 (t) cc_final: 0.8699 (t) REVERT: A 385 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8072 (p) REVERT: A 431 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7462 (mptt) REVERT: A 531 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7804 (m-70) REVERT: A 546 GLU cc_start: 0.8634 (tt0) cc_final: 0.7673 (tm-30) REVERT: A 581 ILE cc_start: 0.9117 (tt) cc_final: 0.8853 (tt) REVERT: A 641 PHE cc_start: 0.6109 (OUTLIER) cc_final: 0.5704 (m-80) REVERT: A 690 PHE cc_start: 0.8176 (t80) cc_final: 0.7888 (t80) REVERT: B 69 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8580 (p) REVERT: B 171 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8357 (t80) REVERT: B 210 GLU cc_start: 0.9052 (mp0) cc_final: 0.8808 (mp0) REVERT: B 236 VAL cc_start: 0.6563 (OUTLIER) cc_final: 0.6209 (m) REVERT: B 328 LEU cc_start: 0.8842 (tp) cc_final: 0.8611 (tt) REVERT: B 339 THR cc_start: 0.8897 (t) cc_final: 0.8688 (t) REVERT: B 385 SER cc_start: 0.8369 (t) cc_final: 0.7895 (p) REVERT: B 431 LYS cc_start: 0.8037 (tmtt) cc_final: 0.7468 (mptt) REVERT: B 531 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7809 (m-70) REVERT: B 546 GLU cc_start: 0.8631 (tt0) cc_final: 0.7676 (tm-30) REVERT: B 581 ILE cc_start: 0.9114 (tt) cc_final: 0.8858 (tt) REVERT: B 641 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.5669 (m-80) REVERT: B 690 PHE cc_start: 0.8183 (t80) cc_final: 0.7892 (t80) outliers start: 92 outliers final: 50 residues processed: 251 average time/residue: 0.0942 time to fit residues: 35.5859 Evaluate side-chains 233 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU 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 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 134 LEU 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 236 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 HIS ** B 662 GLN ** 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 = 0.3826 r_free = 0.3826 target = 0.135222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.106790 restraints weight = 17886.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110044 restraints weight = 7680.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112095 restraints weight = 4750.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.112995 restraints weight = 3678.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113366 restraints weight = 3275.584| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10906 Z= 0.213 Angle : 0.814 9.128 14824 Z= 0.415 Chirality : 0.047 0.182 1722 Planarity : 0.006 0.067 1808 Dihedral : 8.602 57.759 1474 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.94 % Favored : 86.76 % Rotamer: Outliers : 7.38 % Allowed : 28.65 % Favored : 63.98 % 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: -1.08 (0.24), residues: 1314 helix: 0.59 (0.17), residues: 908 sheet: -5.45 (0.66), residues: 20 loop : -3.71 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.015 0.001 TYR B 215 PHE 0.020 0.002 PHE A 513 TRP 0.017 0.002 TRP B 240 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00487 (10906) covalent geometry : angle 0.81359 (14824) hydrogen bonds : bond 0.05600 ( 640) hydrogen bonds : angle 5.11042 ( 1872) *********************** 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 266 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 181 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8429 (t80) REVERT: A 236 VAL cc_start: 0.6343 (OUTLIER) cc_final: 0.6074 (m) REVERT: A 328 LEU cc_start: 0.8878 (tp) cc_final: 0.8635 (tt) REVERT: A 339 THR cc_start: 0.8951 (t) cc_final: 0.8750 (t) REVERT: A 385 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8140 (p) REVERT: A 531 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7746 (m170) REVERT: A 581 ILE cc_start: 0.9188 (tt) cc_final: 0.8923 (tt) REVERT: A 641 PHE cc_start: 0.6178 (OUTLIER) cc_final: 0.5845 (m-80) REVERT: A 682 GLN cc_start: 0.8783 (pm20) cc_final: 0.8372 (mt0) REVERT: A 690 PHE cc_start: 0.8314 (t80) cc_final: 0.8052 (t80) REVERT: B 171 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8426 (t80) REVERT: B 236 VAL cc_start: 0.6352 (OUTLIER) cc_final: 0.6081 (m) REVERT: B 328 LEU cc_start: 0.8880 (tp) cc_final: 0.8639 (tt) REVERT: B 385 SER cc_start: 0.8400 (t) cc_final: 0.7926 (p) REVERT: B 531 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7735 (m170) REVERT: B 581 ILE cc_start: 0.9176 (tt) cc_final: 0.8929 (tt) REVERT: B 641 PHE cc_start: 0.6178 (OUTLIER) cc_final: 0.5797 (m-80) REVERT: B 682 GLN cc_start: 0.8783 (pm20) cc_final: 0.8372 (mt0) REVERT: B 690 PHE cc_start: 0.8317 (t80) cc_final: 0.8055 (t80) outliers start: 85 outliers final: 63 residues processed: 242 average time/residue: 0.0827 time to fit residues: 30.3732 Evaluate side-chains 244 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 172 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 134 LEU 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 176 SER Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 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 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 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 = 0.3882 r_free = 0.3882 target = 0.140190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.109630 restraints weight = 17786.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.113083 restraints weight = 7702.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115294 restraints weight = 4836.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116578 restraints weight = 3777.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.116878 restraints weight = 3321.325| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10906 Z= 0.166 Angle : 0.764 8.996 14824 Z= 0.388 Chirality : 0.045 0.184 1722 Planarity : 0.006 0.063 1808 Dihedral : 8.270 57.889 1467 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.02 % Favored : 87.67 % Rotamer: Outliers : 6.25 % Allowed : 30.30 % Favored : 63.45 % 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: -0.81 (0.25), residues: 1314 helix: 0.82 (0.18), residues: 900 sheet: -5.01 (0.86), residues: 20 loop : -3.60 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.014 0.001 TYR A 215 PHE 0.016 0.001 PHE A 513 TRP 0.021 0.002 TRP A 240 HIS 0.002 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00362 (10906) covalent geometry : angle 0.76394 (14824) hydrogen bonds : bond 0.05184 ( 640) hydrogen bonds : angle 5.01966 ( 1872) *********************** 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 263 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 191 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8390 (t80) REVERT: A 236 VAL cc_start: 0.6394 (OUTLIER) cc_final: 0.6187 (m) REVERT: A 328 LEU cc_start: 0.8860 (tp) cc_final: 0.8620 (tt) REVERT: A 385 SER cc_start: 0.8459 (t) cc_final: 0.8057 (p) REVERT: A 431 LYS cc_start: 0.8038 (tmtt) cc_final: 0.7418 (mptt) REVERT: A 531 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7739 (m-70) REVERT: A 546 GLU cc_start: 0.8731 (tt0) cc_final: 0.7740 (tm-30) REVERT: A 563 MET cc_start: 0.8479 (tpp) cc_final: 0.8166 (mtt) REVERT: A 581 ILE cc_start: 0.9139 (tt) cc_final: 0.8873 (tt) REVERT: A 641 PHE cc_start: 0.6168 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: A 690 PHE cc_start: 0.8205 (t80) cc_final: 0.7952 (t80) REVERT: B 171 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8407 (t80) REVERT: B 236 VAL cc_start: 0.6401 (OUTLIER) cc_final: 0.6194 (m) REVERT: B 328 LEU cc_start: 0.8855 (tp) cc_final: 0.8612 (tt) REVERT: B 385 SER cc_start: 0.8321 (t) cc_final: 0.7874 (p) REVERT: B 392 ASN cc_start: 0.8238 (t0) cc_final: 0.7996 (t0) REVERT: B 431 LYS cc_start: 0.8036 (tmtt) cc_final: 0.7416 (mptt) REVERT: B 531 HIS cc_start: 0.8129 (OUTLIER) cc_final: 0.7741 (m-70) REVERT: B 546 GLU cc_start: 0.8721 (tt0) cc_final: 0.7738 (tm-30) REVERT: B 581 ILE cc_start: 0.9135 (tt) cc_final: 0.8892 (tt) REVERT: B 641 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.5891 (m-80) REVERT: B 690 PHE cc_start: 0.8210 (t80) cc_final: 0.7963 (t80) outliers start: 72 outliers final: 47 residues processed: 249 average time/residue: 0.0885 time to fit residues: 32.9648 Evaluate side-chains 233 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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 207 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 134 LEU 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 236 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 1.9990 chunk 121 optimal weight: 0.0030 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 0.0470 chunk 92 optimal weight: 7.9990 overall best weight: 0.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 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 = 0.3916 r_free = 0.3916 target = 0.142919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112817 restraints weight = 17674.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116351 restraints weight = 7586.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.118644 restraints weight = 4709.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.119782 restraints weight = 3646.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.120395 restraints weight = 3225.745| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10906 Z= 0.158 Angle : 0.759 8.827 14824 Z= 0.386 Chirality : 0.044 0.203 1722 Planarity : 0.006 0.061 1808 Dihedral : 8.222 59.906 1466 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.64 % Favored : 88.05 % Rotamer: Outliers : 5.56 % Allowed : 30.47 % Favored : 63.98 % 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: -0.74 (0.25), residues: 1314 helix: 0.88 (0.18), residues: 898 sheet: -4.91 (0.94), residues: 20 loop : -3.60 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.013 0.001 TYR B 215 PHE 0.018 0.001 PHE B 224 TRP 0.025 0.002 TRP B 349 HIS 0.002 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00335 (10906) covalent geometry : angle 0.75901 (14824) hydrogen bonds : bond 0.04988 ( 640) hydrogen bonds : angle 4.98776 ( 1872) *********************** 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 265 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8754 (p) cc_final: 0.8512 (p) REVERT: A 107 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6371 (tp) REVERT: A 171 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.8286 (t80) REVERT: A 328 LEU cc_start: 0.8833 (tp) cc_final: 0.8598 (tt) REVERT: A 385 SER cc_start: 0.8419 (t) cc_final: 0.8011 (p) REVERT: A 431 LYS cc_start: 0.8005 (tmtt) cc_final: 0.7451 (mptt) REVERT: A 531 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7795 (m-70) REVERT: A 546 GLU cc_start: 0.8686 (tt0) cc_final: 0.7713 (tm-30) REVERT: A 573 SER cc_start: 0.9445 (t) cc_final: 0.8974 (m) REVERT: A 581 ILE cc_start: 0.9089 (tt) cc_final: 0.8832 (tt) REVERT: A 641 PHE cc_start: 0.6106 (OUTLIER) cc_final: 0.5673 (m-80) REVERT: A 682 GLN cc_start: 0.8881 (pm20) cc_final: 0.8341 (mt0) REVERT: A 690 PHE cc_start: 0.8194 (t80) cc_final: 0.7956 (t80) REVERT: B 23 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8695 (tt) REVERT: B 79 VAL cc_start: 0.8753 (p) cc_final: 0.8512 (p) REVERT: B 107 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6145 (tp) REVERT: B 171 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.8283 (t80) REVERT: B 328 LEU cc_start: 0.8830 (tp) cc_final: 0.8596 (tt) REVERT: B 385 SER cc_start: 0.8252 (t) cc_final: 0.7782 (p) REVERT: B 392 ASN cc_start: 0.8213 (t0) cc_final: 0.7952 (t0) REVERT: B 431 LYS cc_start: 0.8003 (tmtt) cc_final: 0.7447 (mptt) REVERT: B 531 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7812 (m-70) REVERT: B 546 GLU cc_start: 0.8680 (tt0) cc_final: 0.7714 (tm-30) REVERT: B 573 SER cc_start: 0.9420 (t) cc_final: 0.8959 (m) REVERT: B 581 ILE cc_start: 0.9074 (tt) cc_final: 0.8835 (tt) REVERT: B 641 PHE cc_start: 0.6124 (OUTLIER) cc_final: 0.5781 (m-80) REVERT: B 682 GLN cc_start: 0.8882 (pm20) cc_final: 0.8338 (mt0) REVERT: B 690 PHE cc_start: 0.8214 (t80) cc_final: 0.7960 (t80) outliers start: 64 outliers final: 43 residues processed: 249 average time/residue: 0.0798 time to fit residues: 29.9777 Evaluate side-chains 232 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 207 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 134 LEU 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 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 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 = 0.3939 r_free = 0.3939 target = 0.143369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.113390 restraints weight = 17583.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.116951 restraints weight = 7597.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.119217 restraints weight = 4741.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.120044 restraints weight = 3682.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121113 restraints weight = 3317.644| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10906 Z= 0.167 Angle : 0.765 7.972 14824 Z= 0.392 Chirality : 0.045 0.196 1722 Planarity : 0.006 0.060 1808 Dihedral : 7.840 59.656 1460 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.87 % Favored : 87.82 % Rotamer: Outliers : 5.82 % Allowed : 30.12 % Favored : 64.06 % 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: -0.78 (0.24), residues: 1314 helix: 0.84 (0.18), residues: 902 sheet: -4.41 (1.06), residues: 20 loop : -3.66 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 56 TYR 0.013 0.001 TYR B 215 PHE 0.018 0.001 PHE B 224 TRP 0.026 0.002 TRP A 349 HIS 0.002 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00361 (10906) covalent geometry : angle 0.76528 (14824) hydrogen bonds : bond 0.04954 ( 640) hydrogen bonds : angle 5.00859 ( 1872) *********************** 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 255 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 188 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8313 (t80) REVERT: A 328 LEU cc_start: 0.8856 (tp) cc_final: 0.8624 (tt) REVERT: A 385 SER cc_start: 0.8399 (t) cc_final: 0.8012 (p) REVERT: A 431 LYS cc_start: 0.8019 (tmtt) cc_final: 0.7459 (mptt) REVERT: A 531 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7811 (m-70) REVERT: A 546 GLU cc_start: 0.8636 (tt0) cc_final: 0.7680 (tm-30) REVERT: A 573 SER cc_start: 0.9414 (t) cc_final: 0.8896 (m) REVERT: A 581 ILE cc_start: 0.9091 (tt) cc_final: 0.8854 (tt) REVERT: A 641 PHE cc_start: 0.6109 (OUTLIER) cc_final: 0.5546 (m-80) REVERT: A 682 GLN cc_start: 0.8851 (pm20) cc_final: 0.8323 (mt0) REVERT: A 690 PHE cc_start: 0.8354 (t80) cc_final: 0.7824 (t80) REVERT: B 23 LEU cc_start: 0.8972 (tp) cc_final: 0.8765 (tt) REVERT: B 171 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8292 (t80) REVERT: B 328 LEU cc_start: 0.8855 (tp) cc_final: 0.8623 (tt) REVERT: B 385 SER cc_start: 0.8280 (t) cc_final: 0.7809 (p) REVERT: B 392 ASN cc_start: 0.8168 (t0) cc_final: 0.7903 (t0) REVERT: B 431 LYS cc_start: 0.8019 (tmtt) cc_final: 0.7456 (mptt) REVERT: B 531 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7836 (m-70) REVERT: B 546 GLU cc_start: 0.8619 (tt0) cc_final: 0.7673 (tm-30) REVERT: B 573 SER cc_start: 0.9398 (t) cc_final: 0.8930 (m) REVERT: B 581 ILE cc_start: 0.9115 (tt) cc_final: 0.8905 (tt) REVERT: B 641 PHE cc_start: 0.6129 (OUTLIER) cc_final: 0.5635 (m-80) REVERT: B 682 GLN cc_start: 0.8850 (pm20) cc_final: 0.8317 (mt0) outliers start: 67 outliers final: 51 residues processed: 236 average time/residue: 0.0821 time to fit residues: 28.7817 Evaluate side-chains 238 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 183 MET Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 134 LEU 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 183 MET Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 691 ARG 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: 5.9990 chunk 20 optimal weight: 0.0030 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 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 = 0.3838 r_free = 0.3838 target = 0.136450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107477 restraints weight = 17537.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110700 restraints weight = 7735.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112743 restraints weight = 4830.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113557 restraints weight = 3752.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.114379 restraints weight = 3356.140| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10906 Z= 0.236 Angle : 0.823 8.827 14824 Z= 0.424 Chirality : 0.047 0.194 1722 Planarity : 0.006 0.060 1808 Dihedral : 7.881 59.633 1460 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.25 % Favored : 87.44 % Rotamer: Outliers : 5.90 % Allowed : 30.38 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.24), residues: 1314 helix: 0.85 (0.18), residues: 890 sheet: -3.80 (1.18), residues: 20 loop : -3.60 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.016 0.001 TYR B 225 PHE 0.020 0.002 PHE B 513 TRP 0.026 0.002 TRP A 240 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00546 (10906) covalent geometry : angle 0.82309 (14824) hydrogen bonds : bond 0.05335 ( 640) hydrogen bonds : angle 5.08771 ( 1872) ********************** 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 250 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 182 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8592 (mp) REVERT: A 171 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8394 (t80) REVERT: A 328 LEU cc_start: 0.8883 (tp) cc_final: 0.8627 (tt) REVERT: A 385 SER cc_start: 0.8502 (t) cc_final: 0.8050 (p) REVERT: A 431 LYS cc_start: 0.7997 (tmtt) cc_final: 0.7355 (mptt) REVERT: A 531 HIS cc_start: 0.8178 (OUTLIER) cc_final: 0.7836 (m-70) REVERT: A 546 GLU cc_start: 0.8686 (tt0) cc_final: 0.7734 (tm-30) REVERT: A 573 SER cc_start: 0.9515 (t) cc_final: 0.8938 (m) REVERT: A 581 ILE cc_start: 0.9161 (tt) cc_final: 0.8924 (tt) REVERT: A 641 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.5612 (m-80) REVERT: A 682 GLN cc_start: 0.8851 (pm20) cc_final: 0.8296 (mt0) REVERT: A 690 PHE cc_start: 0.8352 (t80) cc_final: 0.8049 (t80) REVERT: B 46 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8598 (mp) REVERT: B 171 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8399 (t80) REVERT: B 328 LEU cc_start: 0.8880 (tp) cc_final: 0.8626 (tt) REVERT: B 385 SER cc_start: 0.8312 (t) cc_final: 0.7850 (p) REVERT: B 392 ASN cc_start: 0.8244 (t0) cc_final: 0.7976 (t0) REVERT: B 431 LYS cc_start: 0.7993 (tmtt) cc_final: 0.7347 (mptt) REVERT: B 531 HIS cc_start: 0.8157 (OUTLIER) cc_final: 0.7818 (m-70) REVERT: B 546 GLU cc_start: 0.8673 (tt0) cc_final: 0.7731 (tm-30) REVERT: B 581 ILE cc_start: 0.9171 (tt) cc_final: 0.8955 (tt) REVERT: B 641 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5720 (m-80) REVERT: B 682 GLN cc_start: 0.8847 (pm20) cc_final: 0.8290 (mt0) outliers start: 68 outliers final: 54 residues processed: 231 average time/residue: 0.0783 time to fit residues: 27.4344 Evaluate side-chains 239 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 177 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 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 153 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 134 LEU 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 176 SER Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 691 ARG 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: 3.9990 chunk 19 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN A 476 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.141433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.111345 restraints weight = 17700.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.114818 restraints weight = 7721.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117023 restraints weight = 4840.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.117815 restraints weight = 3771.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.118858 restraints weight = 3401.878| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10906 Z= 0.175 Angle : 0.791 9.720 14824 Z= 0.404 Chirality : 0.046 0.271 1722 Planarity : 0.006 0.058 1808 Dihedral : 7.876 59.999 1460 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.02 % Favored : 87.67 % Rotamer: Outliers : 5.56 % Allowed : 30.90 % Favored : 63.54 % 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: -0.70 (0.25), residues: 1314 helix: 0.85 (0.18), residues: 900 sheet: -3.51 (1.14), residues: 20 loop : -3.52 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 226 TYR 0.016 0.001 TYR B 456 PHE 0.017 0.001 PHE B 513 TRP 0.027 0.002 TRP B 349 HIS 0.002 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00388 (10906) covalent geometry : angle 0.79096 (14824) hydrogen bonds : bond 0.05157 ( 640) hydrogen bonds : angle 5.02237 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1988.22 seconds wall clock time: 35 minutes 11.82 seconds (2111.82 seconds total)