Starting phenix.real_space_refine on Tue May 13 13:53:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gso_34237/05_2025/8gso_34237_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gso_34237/05_2025/8gso_34237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gso_34237/05_2025/8gso_34237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gso_34237/05_2025/8gso_34237.map" model { file = "/net/cci-nas-00/data/ceres_data/8gso_34237/05_2025/8gso_34237_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gso_34237/05_2025/8gso_34237_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 7060 2.51 5 N 1700 2.21 5 O 1828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.48, per 1000 atoms: 0.61 Number of scatterers: 10624 At special positions: 0 Unit cell: (119.262, 112.59, 100.914, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1828 8.00 N 1700 7.00 C 7060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.4 seconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 71.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 80 through 110 Proline residue: A 104 - end of helix Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.536A pdb=" N ASN A 136 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 183 removed outlier: 4.529A pdb=" N VAL A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.044A pdb=" N GLU A 232 " --> pdb=" O VAL A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.732A pdb=" N ASN A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 348 through 353 removed outlier: 4.368A pdb=" N ASN A 353 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 389 Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.628A pdb=" N GLN A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 395' Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.589A pdb=" N MET A 428 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 444 through 484 removed outlier: 4.020A pdb=" N LYS A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 483 " --> pdb=" O LYS A 479 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 523 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 523 through 537 removed outlier: 4.428A pdb=" N LYS A 535 " --> pdb=" O HIS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.583A pdb=" N VAL A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 582 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 612 through 638 removed outlier: 4.234A pdb=" N LEU A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 646 through 665 removed outlier: 3.796A pdb=" N LEU A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 689 through 693 removed outlier: 3.555A pdb=" N TYR A 693 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 28 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 80 through 110 Proline residue: B 104 - end of helix Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.536A pdb=" N ASN B 136 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 183 removed outlier: 4.529A pdb=" N VAL B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 229 through 232 removed outlier: 4.044A pdb=" N GLU B 232 " --> pdb=" O VAL B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.732A pdb=" N ASN B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 304 Processing helix chain 'B' and resid 317 through 326 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 4.368A pdb=" N ASN B 353 " --> pdb=" O GLN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 389 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 416 through 438 removed outlier: 3.589A pdb=" N MET B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 444 through 477 Processing helix chain 'B' and resid 489 through 523 Proline residue: B 499 - end of helix Processing helix chain 'B' and resid 523 through 537 removed outlier: 4.428A pdb=" N LYS B 535 " --> pdb=" O HIS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.583A pdb=" N VAL B 544 " --> pdb=" O THR B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 582 through 594 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 612 through 638 removed outlier: 4.234A pdb=" N LEU B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 646 through 665 removed outlier: 3.796A pdb=" N LEU B 654 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 689 through 693 removed outlier: 3.555A pdb=" N TYR B 693 " --> pdb=" O PHE B 690 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1544 1.27 - 1.40: 2908 1.40 - 1.54: 6299 1.54 - 1.68: 95 1.68 - 1.81: 60 Bond restraints: 10906 Sorted by residual: bond pdb=" C PHE A 95 " pdb=" O PHE A 95 " ideal model delta sigma weight residual 1.236 1.133 0.103 1.16e-02 7.43e+03 7.93e+01 bond pdb=" C PHE B 95 " pdb=" O PHE B 95 " ideal model delta sigma weight residual 1.236 1.133 0.103 1.16e-02 7.43e+03 7.93e+01 bond pdb=" C THR B 496 " pdb=" O THR B 496 " ideal model delta sigma weight residual 1.236 1.323 -0.087 1.16e-02 7.43e+03 5.68e+01 bond pdb=" C THR A 496 " pdb=" O THR A 496 " ideal model delta sigma weight residual 1.236 1.323 -0.087 1.16e-02 7.43e+03 5.68e+01 bond pdb=" N THR B 389 " pdb=" CA THR B 389 " ideal model delta sigma weight residual 1.463 1.559 -0.096 1.30e-02 5.92e+03 5.51e+01 ... (remaining 10901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 13746 2.93 - 5.87: 878 5.87 - 8.80: 149 8.80 - 11.74: 41 11.74 - 14.67: 10 Bond angle restraints: 14824 Sorted by residual: angle pdb=" C LEU A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta sigma weight residual 119.56 108.73 10.83 1.02e+00 9.61e-01 1.13e+02 angle pdb=" C LEU B 107 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " ideal model delta sigma weight residual 119.56 108.73 10.83 1.02e+00 9.61e-01 1.13e+02 angle pdb=" N LYS B 145 " pdb=" CA LYS B 145 " pdb=" C LYS B 145 " ideal model delta sigma weight residual 109.96 95.29 14.67 1.49e+00 4.50e-01 9.69e+01 angle pdb=" N LYS A 145 " pdb=" CA LYS A 145 " pdb=" C LYS A 145 " ideal model delta sigma weight residual 109.96 95.29 14.67 1.49e+00 4.50e-01 9.69e+01 angle pdb=" N PHE B 632 " pdb=" CA PHE B 632 " pdb=" C PHE B 632 " ideal model delta sigma weight residual 113.88 101.88 12.00 1.23e+00 6.61e-01 9.51e+01 ... (remaining 14819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4960 17.46 - 34.91: 716 34.91 - 52.37: 485 52.37 - 69.82: 251 69.82 - 87.28: 22 Dihedral angle restraints: 6434 sinusoidal: 2526 harmonic: 3908 Sorted by residual: dihedral pdb=" C ILE B 397 " pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" CB ILE B 397 " ideal model delta harmonic sigma weight residual -122.00 -136.17 14.17 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" C ILE B 379 " pdb=" N ILE B 379 " pdb=" CA ILE B 379 " pdb=" CB ILE B 379 " ideal model delta harmonic sigma weight residual -122.00 -135.10 13.10 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" C ILE A 379 " pdb=" N ILE A 379 " pdb=" CA ILE A 379 " pdb=" CB ILE A 379 " ideal model delta harmonic sigma weight residual -122.00 -135.10 13.10 0 2.50e+00 1.60e-01 2.75e+01 ... (remaining 6431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1305 0.111 - 0.221: 324 0.221 - 0.332: 57 0.332 - 0.442: 26 0.442 - 0.553: 10 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA PRO B 499 " pdb=" N PRO B 499 " pdb=" C PRO B 499 " pdb=" CB PRO B 499 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA PRO A 499 " pdb=" N PRO A 499 " pdb=" C PRO A 499 " pdb=" CB PRO A 499 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA ILE B 397 " pdb=" N ILE B 397 " pdb=" C ILE B 397 " pdb=" CB ILE B 397 " both_signs ideal model delta sigma weight residual False 2.43 1.91 0.52 2.00e-01 2.50e+01 6.74e+00 ... (remaining 1719 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 107 " 0.123 5.00e-02 4.00e+02 1.85e-01 5.50e+01 pdb=" N PRO A 108 " -0.321 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.106 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 107 " -0.123 5.00e-02 4.00e+02 1.85e-01 5.50e+01 pdb=" N PRO B 108 " 0.321 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " -0.106 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 498 " 0.121 5.00e-02 4.00e+02 1.81e-01 5.25e+01 pdb=" N PRO A 499 " -0.313 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " 0.105 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 20 1.93 - 2.68: 842 2.68 - 3.42: 15677 3.42 - 4.16: 27139 4.16 - 4.90: 46532 Nonbonded interactions: 90210 Sorted by model distance: nonbonded pdb=" CZ2 TRP A 240 " pdb=" CE LYS A 294 " model vdw 1.194 3.740 nonbonded pdb=" CZ2 TRP B 240 " pdb=" CE LYS B 294 " model vdw 1.194 3.740 nonbonded pdb=" NE1 TRP A 240 " pdb=" NZ LYS A 294 " model vdw 1.407 3.200 nonbonded pdb=" NE1 TRP B 240 " pdb=" NZ LYS B 294 " model vdw 1.407 3.200 nonbonded pdb=" CE2 TRP B 240 " pdb=" NZ LYS B 294 " model vdw 1.446 3.340 ... (remaining 90205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.050 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.103 10906 Z= 0.963 Angle : 1.663 14.670 14824 Z= 1.143 Chirality : 0.112 0.553 1722 Planarity : 0.014 0.185 1808 Dihedral : 25.120 87.276 3902 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 6.70 % Allowed : 17.05 % Favored : 76.26 % Rotamer: Outliers : 41.49 % Allowed : 12.07 % Favored : 46.44 % Cbeta Deviations : 1.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.18), residues: 1314 helix: -2.57 (0.13), residues: 864 sheet: -6.27 (0.42), residues: 24 loop : -4.97 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 548 HIS 0.005 0.001 HIS B 617 PHE 0.030 0.002 PHE B 513 TYR 0.010 0.002 TYR B 555 ARG 0.002 0.000 ARG B 226 Details of bonding type rmsd hydrogen bonds : bond 0.17560 ( 633) hydrogen bonds : angle 8.36204 ( 1851) covalent geometry : bond 0.01263 (10906) covalent geometry : angle 1.66307 (14824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 478 poor density : 314 time to evaluate : 1.096 Fit side-chains REVERT: A 2 GLU cc_start: 0.4885 (OUTLIER) cc_final: 0.4439 (tt0) REVERT: A 104 PRO cc_start: 0.6399 (OUTLIER) cc_final: 0.5087 (Cg_exo) REVERT: A 120 LYS cc_start: 0.5868 (OUTLIER) cc_final: 0.5664 (mmmt) REVERT: A 169 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7412 (tttm) REVERT: A 204 ASP cc_start: -0.0318 (OUTLIER) cc_final: -0.0536 (t0) REVERT: A 223 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7772 (p) REVERT: A 337 THR cc_start: 0.7627 (m) cc_final: 0.7148 (p) REVERT: A 420 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8096 (mt) REVERT: A 466 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7251 (mp) REVERT: A 481 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8489 (tt) REVERT: A 532 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8004 (mt) REVERT: A 607 GLU cc_start: 0.7583 (tp30) cc_final: 0.7127 (mm-30) REVERT: A 619 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8112 (mmt90) REVERT: B 2 GLU cc_start: 0.4908 (OUTLIER) cc_final: 0.4550 (tt0) REVERT: B 104 PRO cc_start: 0.6415 (OUTLIER) cc_final: 0.5093 (Cg_exo) REVERT: B 169 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7415 (tttm) REVERT: B 204 ASP cc_start: -0.0315 (OUTLIER) cc_final: -0.0536 (t0) REVERT: B 223 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7776 (p) REVERT: B 337 THR cc_start: 0.7632 (m) cc_final: 0.7150 (p) REVERT: B 420 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8114 (mt) REVERT: B 466 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7244 (mp) REVERT: B 532 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7998 (mt) REVERT: B 607 GLU cc_start: 0.7579 (tp30) cc_final: 0.7124 (mm-30) REVERT: B 619 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8107 (mmt90) outliers start: 478 outliers final: 87 residues processed: 634 average time/residue: 0.2346 time to fit residues: 202.7471 Evaluate side-chains 299 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 192 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 PRO Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 499 PRO Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 PRO Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 PRO Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 660 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 136 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN A 596 ASN A 628 GLN B 40 ASN B 136 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN B 596 ASN B 628 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.161661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126519 restraints weight = 13209.845| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.32 r_work: 0.3362 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10906 Z= 0.228 Angle : 0.898 8.618 14824 Z= 0.472 Chirality : 0.051 0.250 1722 Planarity : 0.008 0.088 1808 Dihedral : 13.115 66.186 1635 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 1.29 % Allowed : 13.85 % Favored : 84.86 % Rotamer: Outliers : 10.94 % Allowed : 23.26 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.22), residues: 1314 helix: -0.64 (0.16), residues: 898 sheet: -6.33 (0.37), residues: 24 loop : -4.89 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 49 HIS 0.003 0.001 HIS A 670 PHE 0.024 0.002 PHE B 369 TYR 0.013 0.002 TYR B 572 ARG 0.007 0.001 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.06543 ( 633) hydrogen bonds : angle 5.33114 ( 1851) covalent geometry : bond 0.00483 (10906) covalent geometry : angle 0.89814 (14824) *********************** 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 327 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 201 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: A 72 ASP cc_start: 0.8502 (m-30) cc_final: 0.8114 (t0) REVERT: A 120 LYS cc_start: 0.6337 (OUTLIER) cc_final: 0.5637 (mmmt) REVERT: A 141 ASN cc_start: 0.5279 (t0) cc_final: 0.4825 (t0) REVERT: A 337 THR cc_start: 0.9053 (m) cc_final: 0.8525 (p) REVERT: A 376 PHE cc_start: 0.7807 (m-10) cc_final: 0.7112 (t80) REVERT: A 570 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7685 (t80) REVERT: A 624 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8997 (tp) REVERT: B 47 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: B 59 PHE cc_start: 0.8561 (m-10) cc_final: 0.8343 (m-10) REVERT: B 72 ASP cc_start: 0.8516 (m-30) cc_final: 0.8124 (t0) REVERT: B 141 ASN cc_start: 0.5274 (t0) cc_final: 0.4819 (t0) REVERT: B 337 THR cc_start: 0.9053 (m) cc_final: 0.8498 (p) REVERT: B 376 PHE cc_start: 0.7798 (m-10) cc_final: 0.7115 (t80) REVERT: B 489 MET cc_start: 0.4879 (ptt) cc_final: 0.4675 (ptt) REVERT: B 570 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7682 (t80) REVERT: B 624 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8988 (tp) outliers start: 126 outliers final: 54 residues processed: 305 average time/residue: 0.1701 time to fit residues: 79.0559 Evaluate side-chains 228 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 167 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.155167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120163 restraints weight = 13668.579| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.32 r_work: 0.3285 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10906 Z= 0.193 Angle : 0.788 9.134 14824 Z= 0.409 Chirality : 0.047 0.186 1722 Planarity : 0.006 0.073 1808 Dihedral : 9.993 72.301 1501 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.53 % Allowed : 13.77 % Favored : 85.69 % Rotamer: Outliers : 7.90 % Allowed : 26.48 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.23), residues: 1314 helix: 0.23 (0.17), residues: 890 sheet: -4.73 (1.15), residues: 10 loop : -4.52 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 49 HIS 0.004 0.001 HIS B 531 PHE 0.021 0.002 PHE B 513 TYR 0.009 0.001 TYR A 572 ARG 0.005 0.001 ARG B 678 Details of bonding type rmsd hydrogen bonds : bond 0.05759 ( 633) hydrogen bonds : angle 5.00380 ( 1851) covalent geometry : bond 0.00443 (10906) covalent geometry : angle 0.78797 (14824) *********************** 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 274 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 183 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: A 72 ASP cc_start: 0.8461 (m-30) cc_final: 0.8061 (t0) REVERT: A 141 ASN cc_start: 0.5808 (t0) cc_final: 0.5590 (t0) REVERT: A 351 ASN cc_start: 0.8064 (p0) cc_final: 0.7859 (p0) REVERT: A 376 PHE cc_start: 0.7936 (m-10) cc_final: 0.6894 (t80) REVERT: A 478 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8223 (m) REVERT: A 489 MET cc_start: 0.5153 (OUTLIER) cc_final: 0.4938 (ptt) REVERT: A 573 SER cc_start: 0.9397 (t) cc_final: 0.8936 (m) REVERT: B 47 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: B 63 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7540 (ttp80) REVERT: B 72 ASP cc_start: 0.8460 (m-30) cc_final: 0.8060 (t0) REVERT: B 141 ASN cc_start: 0.5766 (t0) cc_final: 0.5543 (t0) REVERT: B 376 PHE cc_start: 0.7943 (m-10) cc_final: 0.6889 (t80) REVERT: B 573 SER cc_start: 0.9386 (t) cc_final: 0.8929 (m) outliers start: 91 outliers final: 55 residues processed: 258 average time/residue: 0.1748 time to fit residues: 68.8270 Evaluate side-chains 227 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 40 optimal weight: 0.0570 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN A 628 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.119160 restraints weight = 13499.790| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.30 r_work: 0.3271 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10906 Z= 0.170 Angle : 0.748 10.772 14824 Z= 0.385 Chirality : 0.045 0.192 1722 Planarity : 0.006 0.063 1808 Dihedral : 9.097 74.362 1489 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.61 % Allowed : 12.40 % Favored : 86.99 % Rotamer: Outliers : 5.99 % Allowed : 29.17 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.24), residues: 1314 helix: 0.60 (0.18), residues: 880 sheet: -4.64 (1.22), residues: 10 loop : -4.11 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 548 HIS 0.004 0.001 HIS B 531 PHE 0.020 0.001 PHE A 513 TYR 0.008 0.001 TYR A 634 ARG 0.003 0.000 ARG B 558 Details of bonding type rmsd hydrogen bonds : bond 0.05231 ( 633) hydrogen bonds : angle 4.96656 ( 1851) covalent geometry : bond 0.00381 (10906) covalent geometry : angle 0.74818 (14824) *********************** 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 247 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 178 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: A 63 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7558 (ttp80) REVERT: A 72 ASP cc_start: 0.8450 (m-30) cc_final: 0.8065 (t0) REVERT: A 136 ASN cc_start: 0.8169 (t0) cc_final: 0.7543 (t0) REVERT: A 141 ASN cc_start: 0.5783 (t0) cc_final: 0.5396 (t0) REVERT: A 332 MET cc_start: 0.7751 (ppp) cc_final: 0.7331 (ppp) REVERT: A 351 ASN cc_start: 0.8101 (p0) cc_final: 0.7846 (p0) REVERT: A 376 PHE cc_start: 0.7911 (m-10) cc_final: 0.6659 (t80) REVERT: A 390 LEU cc_start: 0.7878 (tp) cc_final: 0.7620 (tp) REVERT: A 475 PHE cc_start: 0.7848 (m-10) cc_final: 0.7565 (m-10) REVERT: A 478 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8151 (m) REVERT: A 489 MET cc_start: 0.4980 (OUTLIER) cc_final: 0.4636 (ptt) REVERT: A 573 SER cc_start: 0.9281 (t) cc_final: 0.8899 (m) REVERT: A 611 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8051 (tpt-90) REVERT: B 47 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: B 63 ARG cc_start: 0.7788 (mtm110) cc_final: 0.7526 (ttp80) REVERT: B 72 ASP cc_start: 0.8450 (m-30) cc_final: 0.8063 (t0) REVERT: B 141 ASN cc_start: 0.5811 (t0) cc_final: 0.5462 (t0) REVERT: B 332 MET cc_start: 0.7759 (ppp) cc_final: 0.7341 (ppp) REVERT: B 376 PHE cc_start: 0.7908 (m-10) cc_final: 0.6671 (t80) REVERT: B 573 SER cc_start: 0.9286 (t) cc_final: 0.8919 (m) REVERT: B 611 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8060 (tpt-90) outliers start: 69 outliers final: 40 residues processed: 229 average time/residue: 0.1767 time to fit residues: 61.5627 Evaluate side-chains 197 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 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 326 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 56 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114587 restraints weight = 13513.187| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.30 r_work: 0.3194 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10906 Z= 0.196 Angle : 0.755 9.946 14824 Z= 0.388 Chirality : 0.046 0.195 1722 Planarity : 0.006 0.060 1808 Dihedral : 8.151 78.998 1469 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.68 % Allowed : 12.25 % Favored : 87.06 % Rotamer: Outliers : 7.20 % Allowed : 28.47 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.24), residues: 1314 helix: 0.70 (0.18), residues: 890 sheet: None (None), residues: 0 loop : -3.80 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 548 HIS 0.004 0.001 HIS B 531 PHE 0.024 0.002 PHE B 513 TYR 0.007 0.001 TYR B 171 ARG 0.004 0.000 ARG A 678 Details of bonding type rmsd hydrogen bonds : bond 0.05326 ( 633) hydrogen bonds : angle 4.98211 ( 1851) covalent geometry : bond 0.00460 (10906) covalent geometry : angle 0.75481 (14824) *********************** 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 242 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 159 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7810 (mtm110) cc_final: 0.7501 (ttp80) REVERT: A 72 ASP cc_start: 0.8417 (m-30) cc_final: 0.8031 (t0) REVERT: A 141 ASN cc_start: 0.5808 (t0) cc_final: 0.5453 (t0) REVERT: A 188 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8345 (tppt) REVERT: A 332 MET cc_start: 0.7765 (ppp) cc_final: 0.7306 (ppp) REVERT: A 351 ASN cc_start: 0.8397 (p0) cc_final: 0.8150 (p0) REVERT: A 376 PHE cc_start: 0.7881 (m-10) cc_final: 0.6615 (t80) REVERT: A 390 LEU cc_start: 0.7881 (tp) cc_final: 0.7658 (tp) REVERT: A 478 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.8050 (m) REVERT: A 489 MET cc_start: 0.5299 (OUTLIER) cc_final: 0.5043 (ptt) REVERT: A 573 SER cc_start: 0.9353 (t) cc_final: 0.8933 (m) REVERT: A 611 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8291 (tpt-90) REVERT: B 63 ARG cc_start: 0.7750 (mtm110) cc_final: 0.7451 (ttp80) REVERT: B 72 ASP cc_start: 0.8422 (m-30) cc_final: 0.8034 (t0) REVERT: B 141 ASN cc_start: 0.5740 (t0) cc_final: 0.5367 (t0) REVERT: B 188 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8349 (tppt) REVERT: B 332 MET cc_start: 0.7744 (ppp) cc_final: 0.7290 (ppp) REVERT: B 376 PHE cc_start: 0.7878 (m-10) cc_final: 0.6608 (t80) REVERT: B 501 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8267 (p) REVERT: B 573 SER cc_start: 0.9361 (t) cc_final: 0.8932 (m) REVERT: B 611 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8306 (tpt-90) outliers start: 83 outliers final: 53 residues processed: 221 average time/residue: 0.1815 time to fit residues: 59.8903 Evaluate side-chains 209 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 149 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 117 optimal weight: 0.0020 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.9390 ------------------------------------------------------------------------------- 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 237 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 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 = 0.3750 r_free = 0.3750 target = 0.150042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113853 restraints weight = 13596.712| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.36 r_work: 0.3202 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10906 Z= 0.172 Angle : 0.721 8.433 14824 Z= 0.373 Chirality : 0.045 0.183 1722 Planarity : 0.006 0.059 1808 Dihedral : 7.945 84.511 1463 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.10 % Favored : 87.37 % Rotamer: Outliers : 7.12 % Allowed : 28.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.24), residues: 1314 helix: 0.75 (0.17), residues: 904 sheet: None (None), residues: 0 loop : -3.79 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 548 HIS 0.004 0.001 HIS A 531 PHE 0.021 0.001 PHE B 513 TYR 0.006 0.001 TYR B 364 ARG 0.004 0.000 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.05100 ( 633) hydrogen bonds : angle 4.95577 ( 1851) covalent geometry : bond 0.00393 (10906) covalent geometry : angle 0.72127 (14824) *********************** 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 241 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 159 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7944 (tt) REVERT: A 63 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7543 (ttp80) REVERT: A 72 ASP cc_start: 0.8400 (m-30) cc_final: 0.8008 (t0) REVERT: A 141 ASN cc_start: 0.5627 (t0) cc_final: 0.5385 (t0) REVERT: A 188 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8313 (tppt) REVERT: A 332 MET cc_start: 0.7804 (ppp) cc_final: 0.7359 (ppp) REVERT: A 335 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8035 (mmtp) REVERT: A 376 PHE cc_start: 0.7849 (m-10) cc_final: 0.6587 (t80) REVERT: A 478 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.8038 (m) REVERT: A 489 MET cc_start: 0.5182 (OUTLIER) cc_final: 0.4949 (ptt) REVERT: A 573 SER cc_start: 0.9339 (t) cc_final: 0.8910 (m) REVERT: A 611 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8223 (tpt-90) REVERT: B 46 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7923 (tt) REVERT: B 63 ARG cc_start: 0.7791 (mtm110) cc_final: 0.7551 (ttp80) REVERT: B 72 ASP cc_start: 0.8412 (m-30) cc_final: 0.8026 (t0) REVERT: B 141 ASN cc_start: 0.5593 (t0) cc_final: 0.5323 (t0) REVERT: B 188 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8310 (tppt) REVERT: B 332 MET cc_start: 0.7783 (ppp) cc_final: 0.7344 (ppp) REVERT: B 335 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8011 (mmtp) REVERT: B 376 PHE cc_start: 0.7829 (m-10) cc_final: 0.6578 (t80) REVERT: B 501 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8225 (p) REVERT: B 573 SER cc_start: 0.9334 (t) cc_final: 0.8898 (m) REVERT: B 611 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8237 (tpt-90) outliers start: 82 outliers final: 49 residues processed: 219 average time/residue: 0.2112 time to fit residues: 67.0872 Evaluate side-chains 207 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 147 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 93 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 237 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 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 = 0.3732 r_free = 0.3732 target = 0.148315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112030 restraints weight = 13789.907| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.38 r_work: 0.3175 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10906 Z= 0.184 Angle : 0.728 7.992 14824 Z= 0.377 Chirality : 0.045 0.182 1722 Planarity : 0.006 0.056 1808 Dihedral : 7.326 59.361 1456 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.25 % Favored : 87.21 % Rotamer: Outliers : 6.34 % Allowed : 28.65 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.24), residues: 1314 helix: 0.81 (0.17), residues: 904 sheet: None (None), residues: 0 loop : -3.62 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 548 HIS 0.004 0.001 HIS A 531 PHE 0.024 0.001 PHE B 513 TYR 0.008 0.001 TYR B 364 ARG 0.005 0.000 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.05179 ( 633) hydrogen bonds : angle 4.94517 ( 1851) covalent geometry : bond 0.00432 (10906) covalent geometry : angle 0.72815 (14824) *********************** 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 227 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 154 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7556 (ttp80) REVERT: A 72 ASP cc_start: 0.8321 (m-30) cc_final: 0.7960 (t0) REVERT: A 198 ASP cc_start: 0.8264 (t0) cc_final: 0.7915 (t0) REVERT: A 332 MET cc_start: 0.7870 (ppp) cc_final: 0.7433 (ppp) REVERT: A 334 ASP cc_start: 0.7577 (t0) cc_final: 0.7248 (t0) REVERT: A 335 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8105 (mmtp) REVERT: A 376 PHE cc_start: 0.7890 (m-10) cc_final: 0.6644 (t80) REVERT: A 478 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8047 (m) REVERT: A 489 MET cc_start: 0.5302 (OUTLIER) cc_final: 0.5038 (ptt) REVERT: A 573 SER cc_start: 0.9342 (t) cc_final: 0.8903 (m) REVERT: A 611 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8427 (tpt-90) REVERT: B 56 ARG cc_start: 0.7555 (mtp-110) cc_final: 0.7341 (mmm-85) REVERT: B 63 ARG cc_start: 0.7778 (mtm110) cc_final: 0.7523 (ttp80) REVERT: B 72 ASP cc_start: 0.8332 (m-30) cc_final: 0.7966 (t0) REVERT: B 121 ASN cc_start: 0.5036 (OUTLIER) cc_final: 0.4574 (p0) REVERT: B 141 ASN cc_start: 0.5534 (t0) cc_final: 0.5281 (t0) REVERT: B 198 ASP cc_start: 0.8243 (t0) cc_final: 0.7892 (t0) REVERT: B 332 MET cc_start: 0.7863 (ppp) cc_final: 0.7435 (ppp) REVERT: B 334 ASP cc_start: 0.7588 (t0) cc_final: 0.7249 (t0) REVERT: B 335 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8100 (mmtp) REVERT: B 376 PHE cc_start: 0.7887 (m-10) cc_final: 0.6658 (t80) REVERT: B 501 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8234 (p) REVERT: B 573 SER cc_start: 0.9344 (t) cc_final: 0.8900 (m) REVERT: B 611 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8424 (tpt-90) outliers start: 73 outliers final: 52 residues processed: 204 average time/residue: 0.2102 time to fit residues: 62.6071 Evaluate side-chains 209 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 149 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 653 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN ** A 237 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 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113046 restraints weight = 13607.339| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.36 r_work: 0.3191 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10906 Z= 0.171 Angle : 0.725 9.734 14824 Z= 0.374 Chirality : 0.045 0.224 1722 Planarity : 0.005 0.055 1808 Dihedral : 6.936 59.979 1452 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.56 % Favored : 86.99 % Rotamer: Outliers : 5.82 % Allowed : 28.99 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1314 helix: 0.95 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -3.68 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 548 HIS 0.003 0.001 HIS A 531 PHE 0.021 0.001 PHE A 513 TYR 0.007 0.001 TYR B 364 ARG 0.004 0.000 ARG A 318 Details of bonding type rmsd hydrogen bonds : bond 0.05026 ( 633) hydrogen bonds : angle 4.90362 ( 1851) covalent geometry : bond 0.00398 (10906) covalent geometry : angle 0.72538 (14824) *********************** 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 223 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 156 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7838 (mtm110) cc_final: 0.7575 (ttp80) REVERT: A 72 ASP cc_start: 0.8331 (m-30) cc_final: 0.7980 (t0) REVERT: A 198 ASP cc_start: 0.8020 (t0) cc_final: 0.7459 (t0) REVERT: A 332 MET cc_start: 0.7848 (ppp) cc_final: 0.7352 (ppp) REVERT: A 334 ASP cc_start: 0.7407 (t0) cc_final: 0.6871 (t0) REVERT: A 335 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8030 (mmtp) REVERT: A 376 PHE cc_start: 0.7897 (m-10) cc_final: 0.6644 (t80) REVERT: A 478 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.8044 (m) REVERT: A 489 MET cc_start: 0.5456 (OUTLIER) cc_final: 0.5198 (ptt) REVERT: A 573 SER cc_start: 0.9323 (t) cc_final: 0.8894 (m) REVERT: A 685 ASP cc_start: 0.7942 (t0) cc_final: 0.7687 (t70) REVERT: B 63 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7523 (ttp80) REVERT: B 72 ASP cc_start: 0.8344 (m-30) cc_final: 0.7996 (t0) REVERT: B 121 ASN cc_start: 0.4920 (OUTLIER) cc_final: 0.4422 (p0) REVERT: B 198 ASP cc_start: 0.8004 (t0) cc_final: 0.7438 (t0) REVERT: B 332 MET cc_start: 0.7846 (ppp) cc_final: 0.7351 (ppp) REVERT: B 334 ASP cc_start: 0.7416 (t0) cc_final: 0.6873 (t0) REVERT: B 335 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8021 (mmtp) REVERT: B 376 PHE cc_start: 0.7908 (m-10) cc_final: 0.6676 (t80) REVERT: B 501 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 573 SER cc_start: 0.9324 (t) cc_final: 0.8894 (m) outliers start: 67 outliers final: 51 residues processed: 204 average time/residue: 0.2112 time to fit residues: 62.6020 Evaluate side-chains 209 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 152 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 62 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 56 optimal weight: 0.0040 chunk 66 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 141 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.113100 restraints weight = 13807.992| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.38 r_work: 0.3193 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.6980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10906 Z= 0.172 Angle : 0.726 10.048 14824 Z= 0.375 Chirality : 0.045 0.235 1722 Planarity : 0.005 0.052 1808 Dihedral : 6.599 59.885 1448 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.48 % Favored : 87.06 % Rotamer: Outliers : 5.64 % Allowed : 29.34 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1314 helix: 1.07 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -3.65 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 548 HIS 0.004 0.001 HIS A 447 PHE 0.022 0.001 PHE B 513 TYR 0.008 0.001 TYR B 364 ARG 0.010 0.001 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 633) hydrogen bonds : angle 4.90038 ( 1851) covalent geometry : bond 0.00393 (10906) covalent geometry : angle 0.72632 (14824) *********************** 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 227 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7848 (mtm110) cc_final: 0.7589 (ttp80) REVERT: A 72 ASP cc_start: 0.8286 (m-30) cc_final: 0.7942 (t0) REVERT: A 198 ASP cc_start: 0.8103 (t0) cc_final: 0.7513 (t0) REVERT: A 327 SER cc_start: 0.9170 (t) cc_final: 0.8686 (m) REVERT: A 332 MET cc_start: 0.7829 (ppp) cc_final: 0.7380 (ppp) REVERT: A 334 ASP cc_start: 0.7353 (t0) cc_final: 0.6717 (t0) REVERT: A 335 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8016 (mmtp) REVERT: A 376 PHE cc_start: 0.7930 (m-10) cc_final: 0.6731 (t80) REVERT: A 478 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.8059 (m) REVERT: A 489 MET cc_start: 0.5451 (OUTLIER) cc_final: 0.5198 (ptt) REVERT: A 573 SER cc_start: 0.9335 (t) cc_final: 0.8884 (m) REVERT: A 685 ASP cc_start: 0.7918 (t0) cc_final: 0.7659 (t70) REVERT: B 63 ARG cc_start: 0.7822 (mtm110) cc_final: 0.7561 (ttp80) REVERT: B 72 ASP cc_start: 0.8301 (m-30) cc_final: 0.7960 (t0) REVERT: B 198 ASP cc_start: 0.8029 (t0) cc_final: 0.7403 (t0) REVERT: B 327 SER cc_start: 0.9169 (t) cc_final: 0.8677 (m) REVERT: B 332 MET cc_start: 0.7841 (ppp) cc_final: 0.7397 (ppp) REVERT: B 334 ASP cc_start: 0.7347 (t0) cc_final: 0.6686 (t0) REVERT: B 335 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8001 (mmtp) REVERT: B 376 PHE cc_start: 0.7944 (m-10) cc_final: 0.6750 (t80) REVERT: B 501 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8246 (p) REVERT: B 573 SER cc_start: 0.9331 (t) cc_final: 0.8881 (m) REVERT: B 685 ASP cc_start: 0.7885 (t0) cc_final: 0.7642 (t70) outliers start: 65 outliers final: 47 residues processed: 207 average time/residue: 0.2047 time to fit residues: 61.7999 Evaluate side-chains 203 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0570 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.151454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115305 restraints weight = 13483.438| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.36 r_work: 0.3228 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10906 Z= 0.156 Angle : 0.712 9.702 14824 Z= 0.366 Chirality : 0.045 0.201 1722 Planarity : 0.005 0.049 1808 Dihedral : 6.534 58.619 1448 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.40 % Favored : 87.21 % Rotamer: Outliers : 4.60 % Allowed : 30.03 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1314 helix: 1.11 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -3.60 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 548 HIS 0.004 0.001 HIS A 531 PHE 0.019 0.001 PHE A 513 TYR 0.006 0.001 TYR B 517 ARG 0.004 0.001 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 633) hydrogen bonds : angle 4.84350 ( 1851) covalent geometry : bond 0.00350 (10906) covalent geometry : angle 0.71167 (14824) ********************** 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 218 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7848 (mtm110) cc_final: 0.7647 (ttp80) REVERT: A 72 ASP cc_start: 0.8257 (m-30) cc_final: 0.7902 (t0) REVERT: A 136 ASN cc_start: 0.8949 (t0) cc_final: 0.8661 (t0) REVERT: A 198 ASP cc_start: 0.8016 (t0) cc_final: 0.7425 (t0) REVERT: A 327 SER cc_start: 0.9125 (t) cc_final: 0.8568 (m) REVERT: A 332 MET cc_start: 0.7818 (ppp) cc_final: 0.7410 (ppp) REVERT: A 334 ASP cc_start: 0.7266 (t0) cc_final: 0.6619 (t0) REVERT: A 335 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.7944 (mmtp) REVERT: A 364 TYR cc_start: 0.7910 (m-10) cc_final: 0.7703 (m-10) REVERT: A 376 PHE cc_start: 0.7896 (m-10) cc_final: 0.6659 (t80) REVERT: A 478 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.8012 (m) REVERT: A 489 MET cc_start: 0.5448 (OUTLIER) cc_final: 0.5227 (ptt) REVERT: A 573 SER cc_start: 0.9310 (t) cc_final: 0.8868 (m) REVERT: A 685 ASP cc_start: 0.7886 (t0) cc_final: 0.7630 (t70) REVERT: B 63 ARG cc_start: 0.7801 (mtm110) cc_final: 0.7547 (ttp80) REVERT: B 72 ASP cc_start: 0.8265 (m-30) cc_final: 0.7908 (t0) REVERT: B 136 ASN cc_start: 0.8976 (t0) cc_final: 0.8665 (t0) REVERT: B 198 ASP cc_start: 0.8077 (t0) cc_final: 0.7490 (t0) REVERT: B 327 SER cc_start: 0.9132 (t) cc_final: 0.8564 (m) REVERT: B 332 MET cc_start: 0.7821 (ppp) cc_final: 0.7420 (ppp) REVERT: B 334 ASP cc_start: 0.7274 (t0) cc_final: 0.6622 (t0) REVERT: B 335 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.7947 (mmtp) REVERT: B 364 TYR cc_start: 0.7899 (m-10) cc_final: 0.7692 (m-10) REVERT: B 376 PHE cc_start: 0.7888 (m-10) cc_final: 0.6674 (t80) REVERT: B 501 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8200 (p) REVERT: B 573 SER cc_start: 0.9296 (t) cc_final: 0.8848 (m) REVERT: B 685 ASP cc_start: 0.7876 (t0) cc_final: 0.7632 (t70) outliers start: 53 outliers final: 47 residues processed: 205 average time/residue: 0.1854 time to fit residues: 56.6193 Evaluate side-chains 202 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.146296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110252 restraints weight = 13734.227| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.37 r_work: 0.3168 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.7200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10906 Z= 0.209 Angle : 0.755 9.415 14824 Z= 0.392 Chirality : 0.047 0.198 1722 Planarity : 0.006 0.047 1808 Dihedral : 6.359 58.983 1445 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.63 % Favored : 86.99 % Rotamer: Outliers : 4.25 % Allowed : 30.30 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1314 helix: 1.04 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -3.54 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 548 HIS 0.005 0.001 HIS B 447 PHE 0.026 0.002 PHE B 513 TYR 0.014 0.001 TYR A 364 ARG 0.006 0.001 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.05309 ( 633) hydrogen bonds : angle 4.97786 ( 1851) covalent geometry : bond 0.00496 (10906) covalent geometry : angle 0.75480 (14824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5547.84 seconds wall clock time: 96 minutes 54.16 seconds (5814.16 seconds total)