Starting phenix.real_space_refine on Fri Feb 14 20:11:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gro_34210/02_2025/8gro_34210_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gro_34210/02_2025/8gro_34210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gro_34210/02_2025/8gro_34210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gro_34210/02_2025/8gro_34210.map" model { file = "/net/cci-nas-00/data/ceres_data/8gro_34210/02_2025/8gro_34210_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gro_34210/02_2025/8gro_34210_neut.cif" } resolution = 3.5 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 7060 2.51 5 N 1700 2.21 5 O 1828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.64, per 1000 atoms: 0.63 Number of scatterers: 10624 At special positions: 0 Unit cell: (114.258, 114.258, 103.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1828 8.00 N 1700 7.00 C 7060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.5 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 71.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 80 through 110 Proline residue: A 104 - end of helix Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.536A pdb=" N ASN A 136 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 183 removed outlier: 4.529A pdb=" N VAL A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.044A pdb=" N GLU A 232 " --> pdb=" O VAL A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.732A pdb=" N ASN A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 348 through 353 removed outlier: 4.368A pdb=" N ASN A 353 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 389 Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 389 through 396 removed outlier: 4.069A pdb=" N ILE A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.588A pdb=" N MET A 428 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 444 through 482 removed outlier: 3.824A pdb=" N LYS A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 523 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 523 through 537 removed outlier: 4.428A pdb=" N LYS A 535 " --> pdb=" O HIS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.583A pdb=" N VAL A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 582 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 612 through 638 removed outlier: 4.234A pdb=" N LEU A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 646 through 665 removed outlier: 3.795A pdb=" N LEU A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 689 through 693 removed outlier: 3.556A pdb=" N TYR A 693 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 28 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 80 through 110 Proline residue: B 104 - end of helix Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.536A pdb=" N ASN B 136 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 183 removed outlier: 4.529A pdb=" N VAL B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 229 through 232 removed outlier: 4.044A pdb=" N GLU B 232 " --> pdb=" O VAL B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.732A pdb=" N ASN B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 304 Processing helix chain 'B' and resid 317 through 326 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 4.368A pdb=" N ASN B 353 " --> pdb=" O GLN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 389 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 389 through 397 removed outlier: 4.428A pdb=" N ILE B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 416 through 438 removed outlier: 3.588A pdb=" N MET B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 444 through 480 removed outlier: 3.941A pdb=" N LYS B 479 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 523 Proline residue: B 499 - end of helix Processing helix chain 'B' and resid 523 through 537 removed outlier: 4.428A pdb=" N LYS B 535 " --> pdb=" O HIS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.583A pdb=" N VAL B 544 " --> pdb=" O THR B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 582 through 594 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 612 through 638 removed outlier: 4.234A pdb=" N LEU B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 646 through 665 removed outlier: 3.795A pdb=" N LEU B 654 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 689 through 693 removed outlier: 3.556A pdb=" N TYR B 693 " --> pdb=" O PHE B 690 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1542 1.27 - 1.40: 2908 1.40 - 1.54: 6311 1.54 - 1.68: 85 1.68 - 1.81: 60 Bond restraints: 10906 Sorted by residual: bond pdb=" C PHE A 95 " pdb=" O PHE A 95 " ideal model delta sigma weight residual 1.236 1.132 0.104 1.16e-02 7.43e+03 7.97e+01 bond pdb=" C PHE B 95 " pdb=" O PHE B 95 " ideal model delta sigma weight residual 1.236 1.132 0.104 1.16e-02 7.43e+03 7.97e+01 bond pdb=" C THR A 496 " pdb=" O THR A 496 " ideal model delta sigma weight residual 1.236 1.323 -0.087 1.16e-02 7.43e+03 5.58e+01 bond pdb=" C THR B 496 " pdb=" O THR B 496 " ideal model delta sigma weight residual 1.236 1.323 -0.087 1.16e-02 7.43e+03 5.58e+01 bond pdb=" N THR A 389 " pdb=" CA THR A 389 " ideal model delta sigma weight residual 1.463 1.559 -0.096 1.30e-02 5.92e+03 5.50e+01 ... (remaining 10901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 13733 2.93 - 5.87: 887 5.87 - 8.80: 154 8.80 - 11.74: 42 11.74 - 14.67: 8 Bond angle restraints: 14824 Sorted by residual: angle pdb=" C LEU B 107 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " ideal model delta sigma weight residual 119.56 108.71 10.85 1.02e+00 9.61e-01 1.13e+02 angle pdb=" C LEU A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta sigma weight residual 119.56 108.71 10.85 1.02e+00 9.61e-01 1.13e+02 angle pdb=" N LYS A 145 " pdb=" CA LYS A 145 " pdb=" C LYS A 145 " ideal model delta sigma weight residual 109.96 95.29 14.67 1.49e+00 4.50e-01 9.69e+01 angle pdb=" N LYS B 145 " pdb=" CA LYS B 145 " pdb=" C LYS B 145 " ideal model delta sigma weight residual 109.96 95.29 14.67 1.49e+00 4.50e-01 9.69e+01 angle pdb=" N PHE B 632 " pdb=" CA PHE B 632 " pdb=" C PHE B 632 " ideal model delta sigma weight residual 113.88 101.90 11.98 1.23e+00 6.61e-01 9.49e+01 ... (remaining 14819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4945 17.46 - 34.92: 726 34.92 - 52.38: 482 52.38 - 69.84: 259 69.84 - 87.30: 22 Dihedral angle restraints: 6434 sinusoidal: 2526 harmonic: 3908 Sorted by residual: dihedral pdb=" C ILE B 379 " pdb=" N ILE B 379 " pdb=" CA ILE B 379 " pdb=" CB ILE B 379 " ideal model delta harmonic sigma weight residual -122.00 -135.13 13.13 0 2.50e+00 1.60e-01 2.76e+01 dihedral pdb=" C ILE A 379 " pdb=" N ILE A 379 " pdb=" CA ILE A 379 " pdb=" CB ILE A 379 " ideal model delta harmonic sigma weight residual -122.00 -135.13 13.13 0 2.50e+00 1.60e-01 2.76e+01 dihedral pdb=" C VAL A 559 " pdb=" N VAL A 559 " pdb=" CA VAL A 559 " pdb=" CB VAL A 559 " ideal model delta harmonic sigma weight residual -122.00 -134.25 12.25 0 2.50e+00 1.60e-01 2.40e+01 ... (remaining 6431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1301 0.110 - 0.220: 325 0.220 - 0.330: 62 0.330 - 0.440: 26 0.440 - 0.550: 8 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA PRO A 499 " pdb=" N PRO A 499 " pdb=" C PRO A 499 " pdb=" CB PRO A 499 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.57e+00 chirality pdb=" CA PRO B 499 " pdb=" N PRO B 499 " pdb=" C PRO B 499 " pdb=" CB PRO B 499 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.57e+00 chirality pdb=" CA LEU B 103 " pdb=" N LEU B 103 " pdb=" C LEU B 103 " pdb=" CB LEU B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.18e+00 ... (remaining 1719 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 107 " -0.123 5.00e-02 4.00e+02 1.86e-01 5.51e+01 pdb=" N PRO B 108 " 0.321 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " -0.106 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 107 " 0.123 5.00e-02 4.00e+02 1.86e-01 5.51e+01 pdb=" N PRO A 108 " -0.321 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.106 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 498 " 0.121 5.00e-02 4.00e+02 1.81e-01 5.26e+01 pdb=" N PRO B 499 " -0.313 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " 0.105 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.94: 10 1.94 - 2.68: 835 2.68 - 3.42: 15682 3.42 - 4.16: 27148 4.16 - 4.90: 46423 Nonbonded interactions: 90098 Sorted by model distance: nonbonded pdb=" CZ2 TRP B 240 " pdb=" CE LYS B 294 " model vdw 1.194 3.740 nonbonded pdb=" CZ2 TRP A 240 " pdb=" CE LYS A 294 " model vdw 1.194 3.740 nonbonded pdb=" NE1 TRP B 240 " pdb=" NZ LYS B 294 " model vdw 1.408 3.200 nonbonded pdb=" NE1 TRP A 240 " pdb=" NZ LYS A 294 " model vdw 1.408 3.200 nonbonded pdb=" CE2 TRP A 240 " pdb=" NZ LYS A 294 " model vdw 1.446 3.340 ... (remaining 90093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 26.150 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.104 10906 Z= 0.822 Angle : 1.667 14.669 14824 Z= 1.149 Chirality : 0.111 0.550 1722 Planarity : 0.014 0.186 1808 Dihedral : 25.245 87.304 3902 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 6.62 % Allowed : 16.29 % Favored : 77.09 % Rotamer: Outliers : 41.49 % Allowed : 13.11 % Favored : 45.40 % Cbeta Deviations : 1.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.60 (0.13), residues: 876 sheet: -6.27 (0.42), residues: 24 loop : -4.95 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 548 HIS 0.005 0.001 HIS A 617 PHE 0.030 0.002 PHE A 513 TYR 0.010 0.002 TYR B 555 ARG 0.001 0.000 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 478 poor density : 299 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5703 (tt0) REVERT: A 104 PRO cc_start: 0.7192 (OUTLIER) cc_final: 0.5730 (Cg_exo) REVERT: A 144 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6699 (mtmm) REVERT: A 153 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7634 (tp) REVERT: A 187 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8193 (t) REVERT: A 229 VAL cc_start: 0.6806 (OUTLIER) cc_final: 0.6550 (t) REVERT: A 236 VAL cc_start: 0.4525 (OUTLIER) cc_final: 0.4252 (t) REVERT: A 287 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.4398 (mp) REVERT: A 363 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6279 (mt0) REVERT: A 466 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.6823 (mt) REVERT: A 492 ASN cc_start: 0.3974 (OUTLIER) cc_final: 0.3700 (t0) REVERT: A 513 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6231 (t80) REVERT: A 545 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7328 (mmtm) REVERT: A 595 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6946 (ttt90) REVERT: A 641 PHE cc_start: 0.4896 (OUTLIER) cc_final: 0.4302 (m-10) REVERT: A 680 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7580 (mt) REVERT: B 2 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5779 (tt0) REVERT: B 104 PRO cc_start: 0.7174 (OUTLIER) cc_final: 0.5705 (Cg_exo) REVERT: B 144 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6685 (mtmm) REVERT: B 187 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8180 (t) REVERT: B 229 VAL cc_start: 0.6785 (OUTLIER) cc_final: 0.6536 (t) REVERT: B 236 VAL cc_start: 0.4539 (OUTLIER) cc_final: 0.4251 (t) REVERT: B 287 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.4380 (mp) REVERT: B 363 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6329 (mt0) REVERT: B 400 ILE cc_start: 0.6313 (OUTLIER) cc_final: 0.6060 (tt) REVERT: B 466 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.6825 (mt) REVERT: B 492 ASN cc_start: 0.4013 (OUTLIER) cc_final: 0.3710 (t0) REVERT: B 499 PRO cc_start: 0.8688 (OUTLIER) cc_final: 0.8478 (Cg_exo) REVERT: B 513 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6214 (t80) REVERT: B 545 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7323 (mmtm) REVERT: B 595 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6967 (ttt90) REVERT: B 641 PHE cc_start: 0.4862 (OUTLIER) cc_final: 0.4295 (m-10) REVERT: B 680 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7571 (mt) outliers start: 478 outliers final: 120 residues processed: 642 average time/residue: 0.2640 time to fit residues: 229.1832 Evaluate side-chains 337 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 184 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 104 PRO Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 104 PRO Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 499 PRO Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 680 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 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 33 ASN A 40 ASN A 208 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 HIS A 628 GLN A 662 GLN B 33 ASN B 40 ASN B 208 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 HIS B 617 HIS B 628 GLN B 662 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.142233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.112409 restraints weight = 17588.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.115975 restraints weight = 7370.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.118225 restraints weight = 4628.035| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4197 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= 0.319 Angle : 0.915 12.305 14824 Z= 0.478 Chirality : 0.049 0.178 1722 Planarity : 0.007 0.087 1808 Dihedral : 14.852 80.473 1743 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 1.22 % Allowed : 13.09 % Favored : 85.69 % Rotamer: Outliers : 12.76 % Allowed : 23.78 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.05 (0.22), residues: 1314 helix: -0.73 (0.16), residues: 890 sheet: -6.58 (0.29), residues: 24 loop : -4.70 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 613 HIS 0.008 0.001 HIS A 329 PHE 0.022 0.002 PHE A 224 TYR 0.018 0.002 TYR B 215 ARG 0.006 0.001 ARG A 395 *********************** 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 380 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 233 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5755 (tmm) cc_final: 0.5305 (tmm) REVERT: A 171 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8805 (t80) REVERT: A 229 VAL cc_start: 0.7635 (OUTLIER) cc_final: 0.7366 (t) REVERT: A 236 VAL cc_start: 0.6775 (OUTLIER) cc_final: 0.5484 (t) REVERT: A 339 THR cc_start: 0.8916 (t) cc_final: 0.8684 (t) REVERT: A 487 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7989 (mp) REVERT: A 513 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7270 (t80) REVERT: A 545 LYS cc_start: 0.8978 (mmtm) cc_final: 0.8754 (mmmt) REVERT: A 581 ILE cc_start: 0.9057 (tt) cc_final: 0.8833 (tt) REVERT: A 641 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.5447 (m-80) REVERT: A 679 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7686 (pm20) REVERT: A 682 GLN cc_start: 0.8353 (mt0) cc_final: 0.8087 (pp30) REVERT: A 690 PHE cc_start: 0.8060 (t80) cc_final: 0.7754 (t80) REVERT: B 21 MET cc_start: 0.5762 (tmm) cc_final: 0.5316 (tmm) REVERT: B 171 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8801 (t80) REVERT: B 229 VAL cc_start: 0.7636 (OUTLIER) cc_final: 0.7368 (t) REVERT: B 236 VAL cc_start: 0.6769 (OUTLIER) cc_final: 0.5487 (t) REVERT: B 339 THR cc_start: 0.8912 (t) cc_final: 0.8679 (t) REVERT: B 492 ASN cc_start: 0.5840 (OUTLIER) cc_final: 0.5634 (t0) REVERT: B 513 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7258 (t80) REVERT: B 581 ILE cc_start: 0.9059 (tt) cc_final: 0.8838 (tt) REVERT: B 641 PHE cc_start: 0.6155 (OUTLIER) cc_final: 0.5490 (m-80) REVERT: B 679 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7690 (pm20) REVERT: B 682 GLN cc_start: 0.8365 (mt0) cc_final: 0.8081 (pp30) REVERT: B 690 PHE cc_start: 0.8058 (t80) cc_final: 0.7752 (t80) outliers start: 147 outliers final: 66 residues processed: 336 average time/residue: 0.1885 time to fit residues: 93.9789 Evaluate side-chains 258 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 180 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 ASN 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 183 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.141327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.112213 restraints weight = 17914.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.115744 restraints weight = 7362.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117995 restraints weight = 4551.019| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10906 Z= 0.254 Angle : 0.787 9.010 14824 Z= 0.407 Chirality : 0.046 0.219 1722 Planarity : 0.006 0.081 1808 Dihedral : 11.062 57.498 1526 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.68 % Allowed : 12.33 % Favored : 86.99 % Rotamer: Outliers : 8.07 % Allowed : 27.60 % 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: -2.08 (0.23), residues: 1314 helix: -0.06 (0.17), residues: 900 sheet: -6.43 (0.34), residues: 24 loop : -4.25 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 613 HIS 0.007 0.001 HIS B 329 PHE 0.016 0.001 PHE B 224 TYR 0.015 0.001 TYR B 215 ARG 0.005 0.001 ARG A 395 *********************** 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 308 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 215 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.9000 (OUTLIER) cc_final: 0.8670 (p) REVERT: A 112 THR cc_start: 0.8606 (p) cc_final: 0.8404 (p) REVERT: A 153 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7716 (tp) REVERT: A 171 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8543 (t80) REVERT: A 190 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8429 (pp20) REVERT: A 236 VAL cc_start: 0.6223 (OUTLIER) cc_final: 0.5042 (t) REVERT: A 339 THR cc_start: 0.8928 (t) cc_final: 0.8711 (t) REVERT: A 385 SER cc_start: 0.8583 (t) cc_final: 0.8162 (p) REVERT: A 431 LYS cc_start: 0.8033 (tmtt) cc_final: 0.7468 (mptt) REVERT: A 581 ILE cc_start: 0.9079 (tt) cc_final: 0.8830 (tt) REVERT: A 612 MET cc_start: 0.8707 (tpt) cc_final: 0.8424 (tpt) REVERT: A 641 PHE cc_start: 0.6111 (OUTLIER) cc_final: 0.5507 (m-80) REVERT: A 679 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 690 PHE cc_start: 0.8058 (t80) cc_final: 0.7751 (t80) REVERT: B 69 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8565 (p) REVERT: B 112 THR cc_start: 0.8605 (p) cc_final: 0.8404 (p) REVERT: B 171 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8544 (t80) REVERT: B 190 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8438 (pp20) REVERT: B 236 VAL cc_start: 0.6236 (OUTLIER) cc_final: 0.5054 (t) REVERT: B 339 THR cc_start: 0.8922 (t) cc_final: 0.8704 (t) REVERT: B 385 SER cc_start: 0.8506 (t) cc_final: 0.8086 (p) REVERT: B 431 LYS cc_start: 0.8044 (tmtt) cc_final: 0.7476 (mptt) REVERT: B 496 THR cc_start: 0.8667 (m) cc_final: 0.8435 (p) REVERT: B 545 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8711 (mmtt) REVERT: B 581 ILE cc_start: 0.9080 (tt) cc_final: 0.8830 (tt) REVERT: B 612 MET cc_start: 0.8703 (tpt) cc_final: 0.8414 (tpt) REVERT: B 641 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.5510 (m-80) REVERT: B 679 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7804 (mm-30) REVERT: B 690 PHE cc_start: 0.8057 (t80) cc_final: 0.7748 (t80) outliers start: 93 outliers final: 55 residues processed: 278 average time/residue: 0.1986 time to fit residues: 81.6662 Evaluate side-chains 242 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 176 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN 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 183 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 48 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN A 531 HIS A 662 GLN A 670 HIS A 682 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 ASN B 531 HIS B 662 GLN B 670 HIS B 682 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109027 restraints weight = 17113.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.112523 restraints weight = 7177.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114741 restraints weight = 4373.868| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10906 Z= 0.239 Angle : 0.758 9.748 14824 Z= 0.390 Chirality : 0.045 0.244 1722 Planarity : 0.006 0.075 1808 Dihedral : 9.997 59.484 1500 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.80 % Favored : 87.60 % Rotamer: Outliers : 7.90 % Allowed : 26.65 % 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: -1.62 (0.24), residues: 1314 helix: 0.22 (0.17), residues: 920 sheet: -6.41 (0.35), residues: 24 loop : -4.09 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 613 HIS 0.002 0.001 HIS B 329 PHE 0.016 0.001 PHE A 513 TYR 0.015 0.001 TYR B 215 ARG 0.004 0.001 ARG A 395 *********************** 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 290 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 199 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8515 (p) REVERT: A 171 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8404 (t80) REVERT: A 210 GLU cc_start: 0.9118 (mp0) cc_final: 0.8797 (mp0) REVERT: A 236 VAL cc_start: 0.6306 (OUTLIER) cc_final: 0.5830 (m) REVERT: A 328 LEU cc_start: 0.8819 (tp) cc_final: 0.8607 (tt) REVERT: A 339 THR cc_start: 0.8854 (t) cc_final: 0.8646 (t) REVERT: A 385 SER cc_start: 0.8522 (t) cc_final: 0.8030 (p) REVERT: A 581 ILE cc_start: 0.9073 (tt) cc_final: 0.8799 (tt) REVERT: A 641 PHE cc_start: 0.6016 (OUTLIER) cc_final: 0.5516 (m-80) REVERT: A 682 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: A 690 PHE cc_start: 0.8135 (t80) cc_final: 0.7805 (t80) REVERT: B 69 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8577 (p) REVERT: B 171 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8404 (t80) REVERT: B 210 GLU cc_start: 0.9124 (mp0) cc_final: 0.8801 (mp0) REVERT: B 236 VAL cc_start: 0.6325 (OUTLIER) cc_final: 0.5851 (m) REVERT: B 328 LEU cc_start: 0.8810 (tp) cc_final: 0.8601 (tt) REVERT: B 339 THR cc_start: 0.8846 (t) cc_final: 0.8638 (t) REVERT: B 385 SER cc_start: 0.8326 (t) cc_final: 0.7840 (p) REVERT: B 496 THR cc_start: 0.8748 (m) cc_final: 0.8489 (p) REVERT: B 563 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7988 (mtt) REVERT: B 581 ILE cc_start: 0.9072 (tt) cc_final: 0.8800 (tt) REVERT: B 612 MET cc_start: 0.8701 (tpt) cc_final: 0.8493 (tpt) REVERT: B 641 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.5505 (m-80) REVERT: B 682 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7831 (mt0) REVERT: B 690 PHE cc_start: 0.8138 (t80) cc_final: 0.7808 (t80) outliers start: 91 outliers final: 49 residues processed: 270 average time/residue: 0.2108 time to fit residues: 83.4844 Evaluate side-chains 239 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 179 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU 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 207 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 682 GLN Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 56 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 GLN A 682 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.141842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.112280 restraints weight = 17556.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.115859 restraints weight = 7460.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.118109 restraints weight = 4647.264| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10906 Z= 0.242 Angle : 0.771 8.625 14824 Z= 0.391 Chirality : 0.046 0.224 1722 Planarity : 0.006 0.072 1808 Dihedral : 9.350 59.740 1482 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.64 % Favored : 87.90 % Rotamer: Outliers : 7.55 % Allowed : 27.86 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.30 (0.24), residues: 1314 helix: 0.43 (0.17), residues: 920 sheet: -5.69 (0.52), residues: 20 loop : -3.95 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 613 HIS 0.003 0.001 HIS B 531 PHE 0.016 0.001 PHE B 513 TYR 0.021 0.001 TYR A 215 ARG 0.003 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 185 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8514 (p) REVERT: A 171 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8458 (t80) REVERT: A 210 GLU cc_start: 0.9049 (mp0) cc_final: 0.8838 (mp0) REVERT: A 236 VAL cc_start: 0.6339 (OUTLIER) cc_final: 0.6025 (m) REVERT: A 328 LEU cc_start: 0.8838 (tp) cc_final: 0.8598 (tt) REVERT: A 385 SER cc_start: 0.8565 (t) cc_final: 0.8093 (p) REVERT: A 431 LYS cc_start: 0.8041 (tmtt) cc_final: 0.7444 (mptt) REVERT: A 546 GLU cc_start: 0.8692 (tt0) cc_final: 0.7722 (tm-30) REVERT: A 581 ILE cc_start: 0.9129 (tt) cc_final: 0.8868 (tt) REVERT: A 641 PHE cc_start: 0.6094 (OUTLIER) cc_final: 0.5684 (m-80) REVERT: A 690 PHE cc_start: 0.8188 (t80) cc_final: 0.7895 (t80) REVERT: B 69 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8601 (p) REVERT: B 136 ASN cc_start: 0.8544 (t0) cc_final: 0.8336 (t0) REVERT: B 171 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8457 (t80) REVERT: B 210 GLU cc_start: 0.9052 (mp0) cc_final: 0.8840 (mp0) REVERT: B 236 VAL cc_start: 0.6362 (OUTLIER) cc_final: 0.6044 (m) REVERT: B 328 LEU cc_start: 0.8834 (tp) cc_final: 0.8597 (tt) REVERT: B 385 SER cc_start: 0.8366 (t) cc_final: 0.7892 (p) REVERT: B 431 LYS cc_start: 0.8056 (tmtt) cc_final: 0.7457 (mptt) REVERT: B 581 ILE cc_start: 0.9136 (tt) cc_final: 0.8873 (tt) REVERT: B 641 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.5669 (m-80) REVERT: B 690 PHE cc_start: 0.8194 (t80) cc_final: 0.7901 (t80) outliers start: 87 outliers final: 56 residues processed: 248 average time/residue: 0.2012 time to fit residues: 73.5522 Evaluate side-chains 240 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN 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 171 TYR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 117 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.146243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.116731 restraints weight = 17705.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.120345 restraints weight = 7562.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.122622 restraints weight = 4694.639| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10906 Z= 0.210 Angle : 0.735 9.323 14824 Z= 0.374 Chirality : 0.044 0.200 1722 Planarity : 0.006 0.069 1808 Dihedral : 8.510 59.444 1476 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.10 % Favored : 87.60 % Rotamer: Outliers : 5.82 % Allowed : 29.25 % Favored : 64.93 % 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: -0.95 (0.24), residues: 1314 helix: 0.70 (0.17), residues: 902 sheet: -5.43 (0.64), residues: 20 loop : -3.65 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 240 HIS 0.001 0.000 HIS A 617 PHE 0.020 0.001 PHE B 224 TYR 0.018 0.001 TYR A 215 ARG 0.003 0.001 ARG A 395 *********************** 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 268 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 201 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8512 (p) REVERT: A 171 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8370 (t80) REVERT: A 236 VAL cc_start: 0.6382 (OUTLIER) cc_final: 0.6069 (m) REVERT: A 328 LEU cc_start: 0.8790 (tp) cc_final: 0.8461 (tt) REVERT: A 385 SER cc_start: 0.8484 (t) cc_final: 0.8069 (p) REVERT: A 431 LYS cc_start: 0.8122 (tmtt) cc_final: 0.7556 (mptt) REVERT: A 581 ILE cc_start: 0.9091 (tt) cc_final: 0.8860 (tt) REVERT: A 612 MET cc_start: 0.8710 (tpt) cc_final: 0.8284 (tpt) REVERT: A 641 PHE cc_start: 0.6118 (OUTLIER) cc_final: 0.5840 (m-80) REVERT: A 682 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8092 (pp30) REVERT: A 690 PHE cc_start: 0.8154 (t80) cc_final: 0.7908 (t80) REVERT: B 136 ASN cc_start: 0.8532 (t0) cc_final: 0.8245 (t0) REVERT: B 171 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8376 (t80) REVERT: B 236 VAL cc_start: 0.6395 (OUTLIER) cc_final: 0.6088 (m) REVERT: B 328 LEU cc_start: 0.8789 (tp) cc_final: 0.8560 (tt) REVERT: B 385 SER cc_start: 0.8254 (t) cc_final: 0.7766 (p) REVERT: B 431 LYS cc_start: 0.8126 (tmtt) cc_final: 0.7556 (mptt) REVERT: B 545 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8700 (mmmm) REVERT: B 581 ILE cc_start: 0.9101 (tt) cc_final: 0.8858 (tt) REVERT: B 612 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8044 (tpt) REVERT: B 641 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: B 682 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8083 (pp30) REVERT: B 690 PHE cc_start: 0.8156 (t80) cc_final: 0.7906 (t80) outliers start: 67 outliers final: 42 residues processed: 249 average time/residue: 0.2132 time to fit residues: 78.2017 Evaluate side-chains 232 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 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 171 TYR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 93 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 20 optimal weight: 0.0030 chunk 39 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 662 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.146106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116911 restraints weight = 17883.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.120465 restraints weight = 7554.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.122720 restraints weight = 4643.860| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.6093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10906 Z= 0.217 Angle : 0.734 9.633 14824 Z= 0.374 Chirality : 0.044 0.202 1722 Planarity : 0.006 0.066 1808 Dihedral : 8.192 58.874 1468 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.11 % Favored : 88.58 % Rotamer: Outliers : 6.08 % Allowed : 29.34 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.78 (0.24), residues: 1314 helix: 0.77 (0.18), residues: 906 sheet: -5.02 (0.81), residues: 20 loop : -3.47 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 240 HIS 0.003 0.001 HIS B 173 PHE 0.016 0.001 PHE A 224 TYR 0.014 0.001 TYR A 215 ARG 0.005 0.000 ARG A 29 *********************** 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 271 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 201 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8500 (p) REVERT: A 101 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8447 (tt) REVERT: A 171 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.8375 (t80) REVERT: A 236 VAL cc_start: 0.6393 (OUTLIER) cc_final: 0.6187 (m) REVERT: A 328 LEU cc_start: 0.8798 (tp) cc_final: 0.8504 (tt) REVERT: A 385 SER cc_start: 0.8480 (t) cc_final: 0.8064 (p) REVERT: A 545 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8706 (mmmt) REVERT: A 546 GLU cc_start: 0.8679 (tt0) cc_final: 0.7710 (tm-30) REVERT: A 581 ILE cc_start: 0.9075 (tt) cc_final: 0.8848 (tt) REVERT: A 641 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: A 690 PHE cc_start: 0.8233 (t80) cc_final: 0.7978 (t80) REVERT: B 101 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8454 (tt) REVERT: B 171 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8372 (t80) REVERT: B 328 LEU cc_start: 0.8810 (tp) cc_final: 0.8518 (tt) REVERT: B 385 SER cc_start: 0.8245 (t) cc_final: 0.7768 (p) REVERT: B 513 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7239 (t80) REVERT: B 581 ILE cc_start: 0.9077 (tt) cc_final: 0.8842 (tt) REVERT: B 612 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8047 (tpt) REVERT: B 641 PHE cc_start: 0.6179 (OUTLIER) cc_final: 0.5865 (m-80) REVERT: B 690 PHE cc_start: 0.8258 (t80) cc_final: 0.8020 (t80) outliers start: 70 outliers final: 43 residues processed: 248 average time/residue: 0.1925 time to fit residues: 70.4361 Evaluate side-chains 241 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 101 LEU 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 183 MET Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS B 191 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.140747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.112302 restraints weight = 17313.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115669 restraints weight = 7326.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117768 restraints weight = 4482.604| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10906 Z= 0.252 Angle : 0.760 9.090 14824 Z= 0.389 Chirality : 0.045 0.187 1722 Planarity : 0.006 0.065 1808 Dihedral : 8.165 59.926 1467 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.19 % Favored : 88.51 % Rotamer: Outliers : 5.47 % Allowed : 30.47 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.59 (0.25), residues: 1314 helix: 0.93 (0.18), residues: 900 sheet: -4.63 (0.90), residues: 20 loop : -3.38 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 240 HIS 0.002 0.001 HIS A 173 PHE 0.019 0.001 PHE B 465 TYR 0.013 0.001 TYR B 215 ARG 0.004 0.000 ARG B 29 *********************** 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 251 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8375 (t80) REVERT: A 328 LEU cc_start: 0.8832 (tp) cc_final: 0.8582 (tt) REVERT: A 339 THR cc_start: 0.8937 (t) cc_final: 0.8726 (t) REVERT: A 385 SER cc_start: 0.8527 (t) cc_final: 0.8053 (p) REVERT: A 431 LYS cc_start: 0.8071 (tmtt) cc_final: 0.7437 (mptt) REVERT: A 546 GLU cc_start: 0.8604 (tt0) cc_final: 0.7651 (tm-30) REVERT: A 573 SER cc_start: 0.9436 (t) cc_final: 0.8966 (m) REVERT: A 581 ILE cc_start: 0.9082 (tt) cc_final: 0.8870 (tt) REVERT: A 641 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.5833 (m-80) REVERT: A 690 PHE cc_start: 0.8501 (t80) cc_final: 0.8220 (t80) REVERT: B 171 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8297 (t80) REVERT: B 328 LEU cc_start: 0.8859 (tp) cc_final: 0.8618 (tt) REVERT: B 385 SER cc_start: 0.8267 (t) cc_final: 0.7765 (p) REVERT: B 431 LYS cc_start: 0.8080 (tmtt) cc_final: 0.7435 (mptt) REVERT: B 573 SER cc_start: 0.9438 (t) cc_final: 0.8935 (m) REVERT: B 581 ILE cc_start: 0.9075 (tt) cc_final: 0.8865 (tt) REVERT: B 641 PHE cc_start: 0.6142 (OUTLIER) cc_final: 0.5722 (m-80) REVERT: B 690 PHE cc_start: 0.8509 (t80) cc_final: 0.8230 (t80) outliers start: 63 outliers final: 44 residues processed: 231 average time/residue: 0.1941 time to fit residues: 66.8111 Evaluate side-chains 233 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE 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 171 TYR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 62 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.142435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.112343 restraints weight = 17871.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115843 restraints weight = 7623.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.117968 restraints weight = 4733.714| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10906 Z= 0.238 Angle : 0.765 7.876 14824 Z= 0.390 Chirality : 0.044 0.198 1722 Planarity : 0.006 0.063 1808 Dihedral : 7.791 59.920 1458 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.57 % Favored : 88.13 % Rotamer: Outliers : 5.21 % Allowed : 31.60 % Favored : 63.19 % 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: -0.61 (0.25), residues: 1314 helix: 0.95 (0.18), residues: 890 sheet: -4.44 (0.92), residues: 20 loop : -3.40 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 349 HIS 0.002 0.001 HIS A 173 PHE 0.015 0.001 PHE A 224 TYR 0.012 0.001 TYR B 215 ARG 0.004 0.000 ARG B 29 *********************** 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 250 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8307 (t80) REVERT: A 328 LEU cc_start: 0.8821 (tp) cc_final: 0.8579 (tt) REVERT: A 385 SER cc_start: 0.8434 (t) cc_final: 0.8017 (p) REVERT: A 431 LYS cc_start: 0.8063 (tmtt) cc_final: 0.7482 (mptt) REVERT: A 546 GLU cc_start: 0.8665 (tt0) cc_final: 0.7692 (tm-30) REVERT: A 573 SER cc_start: 0.9431 (t) cc_final: 0.8966 (m) REVERT: A 581 ILE cc_start: 0.9058 (tt) cc_final: 0.8850 (tt) REVERT: A 641 PHE cc_start: 0.6054 (OUTLIER) cc_final: 0.5688 (m-80) REVERT: A 690 PHE cc_start: 0.8547 (t80) cc_final: 0.8299 (t80) REVERT: A 691 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8113 (mtm-85) REVERT: B 171 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8302 (t80) REVERT: B 228 LEU cc_start: 0.8029 (tt) cc_final: 0.7797 (pt) REVERT: B 328 LEU cc_start: 0.8842 (tp) cc_final: 0.8602 (tt) REVERT: B 385 SER cc_start: 0.8254 (t) cc_final: 0.7764 (p) REVERT: B 431 LYS cc_start: 0.8062 (tmtt) cc_final: 0.7480 (mptt) REVERT: B 573 SER cc_start: 0.9427 (t) cc_final: 0.8928 (m) REVERT: B 581 ILE cc_start: 0.9054 (tt) cc_final: 0.8849 (tt) REVERT: B 641 PHE cc_start: 0.6061 (OUTLIER) cc_final: 0.5636 (m-80) REVERT: B 690 PHE cc_start: 0.8543 (t80) cc_final: 0.8264 (t80) REVERT: B 691 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8103 (mtm-85) outliers start: 60 outliers final: 48 residues processed: 230 average time/residue: 0.1962 time to fit residues: 66.8541 Evaluate side-chains 241 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE 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 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 101 LEU 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 171 TYR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.141795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.111566 restraints weight = 17651.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115024 restraints weight = 7656.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.117121 restraints weight = 4798.935| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10906 Z= 0.253 Angle : 0.769 10.553 14824 Z= 0.394 Chirality : 0.044 0.202 1722 Planarity : 0.006 0.063 1808 Dihedral : 7.783 59.936 1458 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.26 % Favored : 88.43 % Rotamer: Outliers : 5.03 % Allowed : 31.94 % Favored : 63.02 % 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: -0.59 (0.25), residues: 1314 helix: 0.96 (0.18), residues: 890 sheet: -4.19 (0.95), residues: 20 loop : -3.38 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 240 HIS 0.002 0.001 HIS B 173 PHE 0.016 0.001 PHE A 224 TYR 0.012 0.001 TYR A 215 ARG 0.004 0.000 ARG B 29 ********************** 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 249 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 191 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8312 (t80) REVERT: A 328 LEU cc_start: 0.8852 (tp) cc_final: 0.8613 (tt) REVERT: A 385 SER cc_start: 0.8443 (t) cc_final: 0.8035 (p) REVERT: A 431 LYS cc_start: 0.8048 (tmtt) cc_final: 0.7474 (mptt) REVERT: A 573 SER cc_start: 0.9441 (t) cc_final: 0.8964 (m) REVERT: A 581 ILE cc_start: 0.9075 (tt) cc_final: 0.8865 (tt) REVERT: A 641 PHE cc_start: 0.6043 (OUTLIER) cc_final: 0.5568 (m-80) REVERT: A 690 PHE cc_start: 0.8551 (t80) cc_final: 0.8301 (t80) REVERT: A 691 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8119 (mtm-85) REVERT: B 171 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8326 (t80) REVERT: B 328 LEU cc_start: 0.8850 (tp) cc_final: 0.8601 (tt) REVERT: B 385 SER cc_start: 0.8256 (t) cc_final: 0.7746 (p) REVERT: B 431 LYS cc_start: 0.8043 (tmtt) cc_final: 0.7462 (mptt) REVERT: B 573 SER cc_start: 0.9434 (t) cc_final: 0.8917 (m) REVERT: B 581 ILE cc_start: 0.9070 (tt) cc_final: 0.8861 (tt) REVERT: B 641 PHE cc_start: 0.6021 (OUTLIER) cc_final: 0.5492 (m-80) REVERT: B 690 PHE cc_start: 0.8574 (t80) cc_final: 0.8335 (t80) REVERT: B 691 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8121 (mtm-85) outliers start: 58 outliers final: 48 residues processed: 229 average time/residue: 0.2016 time to fit residues: 68.7047 Evaluate side-chains 239 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 101 LEU 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 171 TYR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 9.9990 chunk 89 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.142570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112635 restraints weight = 17615.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.116172 restraints weight = 7558.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.118418 restraints weight = 4673.612| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.6408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10906 Z= 0.228 Angle : 0.767 11.170 14824 Z= 0.392 Chirality : 0.044 0.211 1722 Planarity : 0.006 0.063 1808 Dihedral : 7.737 59.386 1458 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.42 % Favored : 88.28 % Rotamer: Outliers : 4.86 % Allowed : 32.20 % Favored : 62.93 % 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: -0.57 (0.25), residues: 1314 helix: 0.97 (0.18), residues: 892 sheet: -4.19 (0.95), residues: 20 loop : -3.40 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 240 HIS 0.002 0.001 HIS A 173 PHE 0.016 0.001 PHE A 224 TYR 0.013 0.001 TYR B 215 ARG 0.004 0.000 ARG B 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3698.58 seconds wall clock time: 67 minutes 7.59 seconds (4027.59 seconds total)