Starting phenix.real_space_refine on Mon Jul 28 18:45:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gro_34210/07_2025/8gro_34210_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gro_34210/07_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_34210/07_2025/8gro_34210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gro_34210/07_2025/8gro_34210.map" model { file = "/net/cci-nas-00/data/ceres_data/8gro_34210/07_2025/8gro_34210_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gro_34210/07_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-5711/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: 7.56, per 1000 atoms: 0.71 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: 3.99 Conformation dependent library (CDL) restraints added in 2.0 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: 1.22 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: 4.52 Time building geometry restraints manager: 4.15 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: 0.04 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: 210.180 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: 4.440 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.360 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 250.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.104 10906 Z= 0.964 Angle : 1.667 14.669 14824 Z= 1.149 Chirality : 0.111 0.550 1722 Planarity : 0.014 0.186 1808 Dihedral : 25.245 87.304 3902 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 6.62 % Allowed : 16.29 % Favored : 77.09 % Rotamer: Outliers : 41.49 % Allowed : 13.11 % Favored : 45.40 % Cbeta Deviations : 1.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.17115 ( 640) hydrogen bonds : angle 8.32837 ( 1872) covalent geometry : bond 0.01264 (10906) covalent geometry : angle 1.66685 (14824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 478 poor density : 299 time to evaluate : 2.814 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: 0.3184 time to fit residues: 282.9379 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 : 1.393 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.112409 restraints weight = 17588.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.115969 restraints weight = 7370.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.118191 restraints weight = 4637.633| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- 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= 0.226 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 Details of bonding type rmsd hydrogen bonds : bond 0.06647 ( 640) hydrogen bonds : angle 5.31456 ( 1872) covalent geometry : bond 0.00481 (10906) covalent geometry : angle 0.91512 (14824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 233 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5752 (tmm) cc_final: 0.5302 (tmm) REVERT: A 171 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8806 (t80) REVERT: A 229 VAL cc_start: 0.7634 (OUTLIER) cc_final: 0.7365 (t) REVERT: A 236 VAL cc_start: 0.6771 (OUTLIER) cc_final: 0.5478 (t) REVERT: A 339 THR cc_start: 0.8915 (t) cc_final: 0.8683 (t) REVERT: A 487 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7989 (mp) REVERT: A 513 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7269 (t80) REVERT: A 545 LYS cc_start: 0.8977 (mmtm) cc_final: 0.8753 (mmmt) REVERT: A 581 ILE cc_start: 0.9057 (tt) cc_final: 0.8833 (tt) REVERT: A 641 PHE cc_start: 0.6107 (OUTLIER) cc_final: 0.5446 (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: 0.7753 (t80) REVERT: B 21 MET cc_start: 0.5762 (tmm) cc_final: 0.5315 (tmm) REVERT: B 171 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8801 (t80) REVERT: B 229 VAL cc_start: 0.7635 (OUTLIER) cc_final: 0.7368 (t) REVERT: B 236 VAL cc_start: 0.6766 (OUTLIER) cc_final: 0.5485 (t) REVERT: B 339 THR cc_start: 0.8912 (t) cc_final: 0.8679 (t) REVERT: B 492 ASN cc_start: 0.5843 (OUTLIER) cc_final: 0.5637 (t0) REVERT: B 513 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7257 (t80) REVERT: B 581 ILE cc_start: 0.9059 (tt) cc_final: 0.8838 (tt) REVERT: B 641 PHE cc_start: 0.6153 (OUTLIER) cc_final: 0.5489 (m-80) REVERT: B 679 GLU cc_start: 0.8051 (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: 0.2204 time to fit residues: 111.6451 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 : 1.278 ------------------------------------------------------------------------------- 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: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.142382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113247 restraints weight = 17864.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.116863 restraints weight = 7330.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.119100 restraints weight = 4507.481| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10906 Z= 0.175 Angle : 0.785 8.687 14824 Z= 0.405 Chirality : 0.046 0.224 1722 Planarity : 0.006 0.079 1808 Dihedral : 10.961 57.442 1526 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.68 % Allowed : 12.33 % Favored : 86.99 % Rotamer: Outliers : 7.90 % Allowed : 27.86 % Favored : 64.24 % 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: -1.90 (0.23), residues: 1314 helix: 0.01 (0.17), residues: 910 sheet: -5.66 (0.75), residues: 10 loop : -4.23 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 613 HIS 0.006 0.001 HIS B 329 PHE 0.020 0.001 PHE B 224 TYR 0.015 0.001 TYR A 215 ARG 0.005 0.001 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.05575 ( 640) hydrogen bonds : angle 5.09960 ( 1872) covalent geometry : bond 0.00372 (10906) covalent geometry : angle 0.78478 (14824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 214 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.8965 (OUTLIER) cc_final: 0.8579 (p) REVERT: A 171 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8532 (t80) REVERT: A 190 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8347 (pp20) REVERT: A 236 VAL cc_start: 0.6306 (OUTLIER) cc_final: 0.5123 (t) REVERT: A 339 THR cc_start: 0.8932 (t) cc_final: 0.8720 (t) REVERT: A 385 SER cc_start: 0.8526 (t) cc_final: 0.8055 (p) REVERT: A 431 LYS cc_start: 0.8006 (tmtt) cc_final: 0.7469 (mptt) REVERT: A 581 ILE cc_start: 0.9064 (tt) cc_final: 0.8800 (tt) REVERT: A 612 MET cc_start: 0.8686 (tpt) cc_final: 0.8324 (tpt) REVERT: A 641 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5607 (m-80) REVERT: A 679 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7792 (mm-30) REVERT: A 690 PHE cc_start: 0.8058 (t80) cc_final: 0.7768 (t80) REVERT: B 69 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 171 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8536 (t80) REVERT: B 190 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8355 (pp20) REVERT: B 236 VAL cc_start: 0.6321 (OUTLIER) cc_final: 0.5136 (t) REVERT: B 339 THR cc_start: 0.8926 (t) cc_final: 0.8710 (t) REVERT: B 385 SER cc_start: 0.8471 (t) cc_final: 0.8025 (p) REVERT: B 431 LYS cc_start: 0.8016 (tmtt) cc_final: 0.7476 (mptt) REVERT: B 496 THR cc_start: 0.8702 (m) cc_final: 0.8474 (p) REVERT: B 545 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8731 (mmtt) REVERT: B 581 ILE cc_start: 0.9066 (tt) cc_final: 0.8802 (tt) REVERT: B 612 MET cc_start: 0.8678 (tpt) cc_final: 0.8310 (tpt) REVERT: B 641 PHE cc_start: 0.6135 (OUTLIER) cc_final: 0.5596 (m-80) REVERT: B 679 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7790 (mm-30) REVERT: B 690 PHE cc_start: 0.8059 (t80) cc_final: 0.7766 (t80) outliers start: 91 outliers final: 51 residues processed: 276 average time/residue: 0.1909 time to fit residues: 78.0893 Evaluate side-chains 244 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 114 ASN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 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 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 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: 0.9990 chunk 8 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 97 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 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 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 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 662 GLN B 670 HIS B 682 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.138353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109191 restraints weight = 17186.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.112756 restraints weight = 7131.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114980 restraints weight = 4320.405| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10906 Z= 0.165 Angle : 0.764 10.440 14824 Z= 0.388 Chirality : 0.045 0.233 1722 Planarity : 0.006 0.074 1808 Dihedral : 9.821 59.501 1500 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.80 % Favored : 87.60 % Rotamer: Outliers : 7.03 % Allowed : 28.39 % 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: -1.51 (0.24), residues: 1314 helix: 0.28 (0.17), residues: 916 sheet: -6.25 (0.31), residues: 34 loop : -3.79 (0.32), residues: 364 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 224 TYR 0.021 0.001 TYR A 572 ARG 0.004 0.001 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.05205 ( 640) hydrogen bonds : angle 4.94723 ( 1872) covalent geometry : bond 0.00353 (10906) covalent geometry : angle 0.76444 (14824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 204 time to evaluate : 1.135 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: A 171 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8387 (t80) REVERT: A 236 VAL cc_start: 0.6462 (OUTLIER) cc_final: 0.5943 (m) REVERT: A 385 SER cc_start: 0.8497 (t) cc_final: 0.8009 (p) REVERT: A 563 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7990 (mtt) REVERT: A 581 ILE cc_start: 0.9047 (tt) cc_final: 0.8771 (tt) REVERT: A 612 MET cc_start: 0.8708 (tpt) cc_final: 0.8418 (tpt) REVERT: A 641 PHE cc_start: 0.6038 (OUTLIER) cc_final: 0.5592 (m-80) REVERT: A 690 PHE cc_start: 0.8175 (t80) cc_final: 0.7857 (t80) REVERT: B 171 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8386 (t80) REVERT: B 236 VAL cc_start: 0.6476 (OUTLIER) cc_final: 0.5960 (m) REVERT: B 385 SER cc_start: 0.8245 (t) cc_final: 0.7762 (p) REVERT: B 496 THR cc_start: 0.8754 (m) cc_final: 0.8544 (p) REVERT: B 563 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8012 (mtt) REVERT: B 581 ILE cc_start: 0.9043 (tt) cc_final: 0.8767 (tt) REVERT: B 612 MET cc_start: 0.8699 (tpt) cc_final: 0.8414 (tpt) REVERT: B 641 PHE cc_start: 0.6035 (OUTLIER) cc_final: 0.5586 (m-80) REVERT: B 690 PHE cc_start: 0.8179 (t80) cc_final: 0.7860 (t80) outliers start: 81 outliers final: 44 residues processed: 264 average time/residue: 0.2129 time to fit residues: 82.4658 Evaluate side-chains 233 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 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 358 SER Chi-restraints excluded: chain A residue 374 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 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 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 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 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 358 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 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 691 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 56 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 104 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 HIS A 615 HIS A 662 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 531 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.136048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106890 restraints weight = 17282.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110272 restraints weight = 7338.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112445 restraints weight = 4487.578| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10906 Z= 0.182 Angle : 0.766 9.468 14824 Z= 0.391 Chirality : 0.045 0.221 1722 Planarity : 0.006 0.070 1808 Dihedral : 9.035 58.697 1482 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.80 % Favored : 87.75 % Rotamer: Outliers : 7.64 % Allowed : 27.95 % Favored : 64.41 % 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: -1.12 (0.24), residues: 1314 helix: 0.55 (0.17), residues: 914 sheet: -5.61 (0.55), residues: 20 loop : -3.76 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 240 HIS 0.002 0.001 HIS A 447 PHE 0.019 0.001 PHE B 224 TYR 0.020 0.001 TYR A 215 ARG 0.003 0.001 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.05342 ( 640) hydrogen bonds : angle 4.97592 ( 1872) covalent geometry : bond 0.00403 (10906) covalent geometry : angle 0.76558 (14824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 185 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8509 (mp) REVERT: A 69 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8578 (p) REVERT: A 171 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8352 (t80) REVERT: A 210 GLU cc_start: 0.9126 (mp0) cc_final: 0.8813 (mp0) REVERT: A 236 VAL cc_start: 0.6277 (OUTLIER) cc_final: 0.5920 (m) REVERT: A 339 THR cc_start: 0.8902 (t) cc_final: 0.8695 (t) REVERT: A 385 SER cc_start: 0.8477 (t) cc_final: 0.8009 (p) REVERT: A 431 LYS cc_start: 0.7957 (tmtt) cc_final: 0.7327 (mptt) REVERT: A 531 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7693 (m-70) REVERT: A 581 ILE cc_start: 0.9117 (tt) cc_final: 0.8874 (tt) REVERT: A 641 PHE cc_start: 0.6042 (OUTLIER) cc_final: 0.5711 (m-80) REVERT: A 690 PHE cc_start: 0.8250 (t80) cc_final: 0.7869 (t80) REVERT: B 46 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8512 (mp) REVERT: B 69 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8580 (p) REVERT: B 171 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8343 (t80) REVERT: B 210 GLU cc_start: 0.9134 (mp0) cc_final: 0.8814 (mp0) REVERT: B 236 VAL cc_start: 0.6295 (OUTLIER) cc_final: 0.5939 (m) REVERT: B 339 THR cc_start: 0.8894 (t) cc_final: 0.8684 (t) REVERT: B 385 SER cc_start: 0.8288 (t) cc_final: 0.7797 (p) REVERT: B 431 LYS cc_start: 0.7969 (tmtt) cc_final: 0.7336 (mptt) REVERT: B 496 THR cc_start: 0.8794 (m) cc_final: 0.8553 (p) REVERT: B 531 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7682 (m-70) REVERT: B 581 ILE cc_start: 0.9124 (tt) cc_final: 0.8880 (tt) REVERT: B 641 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5793 (m-80) REVERT: B 690 PHE cc_start: 0.8260 (t80) cc_final: 0.7877 (t80) outliers start: 88 outliers final: 54 residues processed: 248 average time/residue: 0.1871 time to fit residues: 69.3306 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 : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 106 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 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 487 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 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 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 46 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 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 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 525 ILE Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 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 691 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 126 optimal weight: 0.4980 chunk 77 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.137692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107426 restraints weight = 17995.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110843 restraints weight = 7659.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.112986 restraints weight = 4783.655| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5844 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= 0.196 Angle : 0.774 8.625 14824 Z= 0.395 Chirality : 0.045 0.188 1722 Planarity : 0.006 0.067 1808 Dihedral : 8.619 58.639 1473 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.10 % Favored : 87.60 % Rotamer: Outliers : 6.42 % Allowed : 29.69 % Favored : 63.89 % 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: -0.93 (0.24), residues: 1314 helix: 0.64 (0.17), residues: 920 sheet: -5.44 (0.62), residues: 20 loop : -3.62 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 548 HIS 0.013 0.002 HIS B 531 PHE 0.018 0.001 PHE A 513 TYR 0.015 0.001 TYR A 215 ARG 0.003 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.05400 ( 640) hydrogen bonds : angle 5.04699 ( 1872) covalent geometry : bond 0.00445 (10906) covalent geometry : angle 0.77425 (14824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 179 time to evaluate : 1.242 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 46 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 69 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8580 (p) REVERT: A 101 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8439 (tt) REVERT: A 171 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8426 (t80) REVERT: A 236 VAL cc_start: 0.6176 (OUTLIER) cc_final: 0.5974 (m) REVERT: A 385 SER cc_start: 0.8553 (t) cc_final: 0.8113 (p) REVERT: A 431 LYS cc_start: 0.8028 (tmtt) cc_final: 0.7458 (mptt) REVERT: A 581 ILE cc_start: 0.9176 (tt) cc_final: 0.8929 (tt) REVERT: A 641 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.5868 (m-80) REVERT: A 690 PHE cc_start: 0.8270 (t80) cc_final: 0.7916 (t80) REVERT: B 46 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8572 (mp) REVERT: B 69 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8582 (p) REVERT: B 101 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8447 (tt) REVERT: B 171 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8418 (t80) REVERT: B 339 THR cc_start: 0.8960 (t) cc_final: 0.8759 (t) REVERT: B 385 SER cc_start: 0.8385 (t) cc_final: 0.7903 (p) REVERT: B 431 LYS cc_start: 0.8038 (tmtt) cc_final: 0.7467 (mptt) REVERT: B 496 THR cc_start: 0.8790 (m) cc_final: 0.8575 (p) REVERT: B 581 ILE cc_start: 0.9182 (tt) cc_final: 0.8934 (tt) REVERT: B 641 PHE cc_start: 0.6145 (OUTLIER) cc_final: 0.5820 (m-80) REVERT: B 690 PHE cc_start: 0.8277 (t80) cc_final: 0.7921 (t80) outliers start: 74 outliers final: 48 residues processed: 232 average time/residue: 0.1932 time to fit residues: 66.2930 Evaluate side-chains 229 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 101 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 153 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 183 MET 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 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 46 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 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 374 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 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 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 93 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.0370 chunk 39 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.141692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.111368 restraints weight = 17999.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114874 restraints weight = 7601.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117107 restraints weight = 4719.068| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10906 Z= 0.156 Angle : 0.754 9.691 14824 Z= 0.381 Chirality : 0.044 0.189 1722 Planarity : 0.006 0.064 1808 Dihedral : 8.190 58.660 1463 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.18 % Favored : 87.52 % Rotamer: Outliers : 6.86 % Allowed : 29.51 % Favored : 63.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.25), residues: 1314 helix: 0.82 (0.18), residues: 902 sheet: -5.18 (0.74), residues: 20 loop : -3.50 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 349 HIS 0.002 0.001 HIS B 531 PHE 0.017 0.001 PHE A 224 TYR 0.014 0.001 TYR B 215 ARG 0.002 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.05027 ( 640) hydrogen bonds : angle 4.97588 ( 1872) covalent geometry : bond 0.00330 (10906) covalent geometry : angle 0.75449 (14824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 190 time to evaluate : 1.325 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 46 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8557 (mp) REVERT: A 101 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8536 (tt) REVERT: A 171 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8390 (t80) REVERT: A 236 VAL cc_start: 0.6251 (OUTLIER) cc_final: 0.6048 (m) REVERT: A 385 SER cc_start: 0.8463 (t) cc_final: 0.8037 (p) REVERT: A 431 LYS cc_start: 0.7966 (tmtt) cc_final: 0.7423 (mptt) REVERT: A 531 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.7742 (m-70) REVERT: A 573 SER cc_start: 0.9457 (t) cc_final: 0.8982 (m) REVERT: A 581 ILE cc_start: 0.9107 (tt) cc_final: 0.8869 (tt) REVERT: A 641 PHE cc_start: 0.6153 (OUTLIER) cc_final: 0.5841 (m-80) REVERT: A 690 PHE cc_start: 0.8151 (t80) cc_final: 0.7886 (t80) REVERT: B 46 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8549 (mp) REVERT: B 101 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8542 (tt) REVERT: B 171 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8380 (t80) REVERT: B 385 SER cc_start: 0.8263 (t) cc_final: 0.7779 (p) REVERT: B 431 LYS cc_start: 0.7969 (tmtt) cc_final: 0.7425 (mptt) REVERT: B 531 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7736 (m-70) REVERT: B 581 ILE cc_start: 0.9104 (tt) cc_final: 0.8872 (tt) REVERT: B 641 PHE cc_start: 0.6134 (OUTLIER) cc_final: 0.5845 (m-80) REVERT: B 690 PHE cc_start: 0.8158 (t80) cc_final: 0.7891 (t80) outliers start: 79 outliers final: 50 residues processed: 249 average time/residue: 0.1899 time to fit residues: 70.5444 Evaluate side-chains 236 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN 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 218 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 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 531 HIS Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 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 218 GLU 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 432 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 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 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 18 optimal weight: 0.0050 chunk 55 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.144187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114386 restraints weight = 17686.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117961 restraints weight = 7521.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120225 restraints weight = 4647.317| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10906 Z= 0.159 Angle : 0.763 10.849 14824 Z= 0.386 Chirality : 0.044 0.186 1722 Planarity : 0.006 0.062 1808 Dihedral : 8.104 59.812 1463 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.34 % Favored : 88.36 % Rotamer: Outliers : 5.90 % Allowed : 30.56 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.72 (0.25), residues: 1314 helix: 0.84 (0.18), residues: 902 sheet: -4.67 (0.86), residues: 20 loop : -3.49 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 349 HIS 0.003 0.001 HIS B 173 PHE 0.020 0.001 PHE A 224 TYR 0.013 0.001 TYR B 215 ARG 0.003 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.04938 ( 640) hydrogen bonds : angle 4.97441 ( 1872) covalent geometry : bond 0.00338 (10906) covalent geometry : angle 0.76254 (14824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 188 time to evaluate : 1.166 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 23 LEU cc_start: 0.8995 (tp) cc_final: 0.8792 (tt) REVERT: A 101 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8547 (tt) REVERT: A 171 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8370 (t80) REVERT: A 385 SER cc_start: 0.8429 (t) cc_final: 0.8034 (p) REVERT: A 431 LYS cc_start: 0.8010 (tmtt) cc_final: 0.7453 (mptt) REVERT: A 531 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7815 (m-70) REVERT: A 570 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7320 (t80) REVERT: A 573 SER cc_start: 0.9392 (t) cc_final: 0.8930 (m) REVERT: A 581 ILE cc_start: 0.9099 (tt) cc_final: 0.8888 (tt) REVERT: A 641 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5746 (m-80) REVERT: A 690 PHE cc_start: 0.8268 (t80) cc_final: 0.8064 (t80) REVERT: B 46 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8600 (mp) REVERT: B 101 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8541 (tt) REVERT: B 171 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8366 (t80) REVERT: B 385 SER cc_start: 0.8275 (t) cc_final: 0.7776 (p) REVERT: B 431 LYS cc_start: 0.8012 (tmtt) cc_final: 0.7454 (mptt) REVERT: B 531 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7812 (m-70) REVERT: B 570 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7360 (t80) REVERT: B 573 SER cc_start: 0.9385 (t) cc_final: 0.8921 (m) REVERT: B 581 ILE cc_start: 0.9095 (tt) cc_final: 0.8883 (tt) REVERT: B 641 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5693 (m-80) REVERT: B 682 GLN cc_start: 0.8625 (pm20) cc_final: 0.8351 (mt0) REVERT: B 690 PHE cc_start: 0.8270 (t80) cc_final: 0.8068 (t80) outliers start: 68 outliers final: 43 residues processed: 236 average time/residue: 0.1893 time to fit residues: 66.3928 Evaluate side-chains 233 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 171 TYR 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 478 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 62 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 117 optimal weight: 0.4980 chunk 107 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** B 463 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 = 0.3910 r_free = 0.3910 target = 0.142338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.111602 restraints weight = 18029.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.115210 restraints weight = 7777.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.117515 restraints weight = 4814.733| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10906 Z= 0.160 Angle : 0.753 8.309 14824 Z= 0.382 Chirality : 0.044 0.199 1722 Planarity : 0.006 0.061 1808 Dihedral : 7.760 59.872 1458 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.34 % Favored : 88.36 % Rotamer: Outliers : 5.64 % Allowed : 31.16 % 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: -0.67 (0.25), residues: 1314 helix: 0.86 (0.18), residues: 902 sheet: -4.70 (0.78), residues: 20 loop : -3.43 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 349 HIS 0.002 0.001 HIS B 173 PHE 0.026 0.001 PHE A 465 TYR 0.020 0.001 TYR A 572 ARG 0.003 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 640) hydrogen bonds : angle 4.98289 ( 1872) covalent geometry : bond 0.00346 (10906) covalent geometry : angle 0.75331 (14824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 189 time to evaluate : 1.101 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 40 ASN cc_start: 0.8589 (t0) cc_final: 0.8327 (t0) REVERT: A 101 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8617 (tt) REVERT: A 171 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8263 (t80) REVERT: A 385 SER cc_start: 0.8417 (t) cc_final: 0.7998 (p) REVERT: A 531 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7769 (m-70) REVERT: A 573 SER cc_start: 0.9390 (t) cc_final: 0.8951 (m) REVERT: A 641 PHE cc_start: 0.6031 (OUTLIER) cc_final: 0.5541 (m-80) REVERT: A 690 PHE cc_start: 0.8265 (t80) cc_final: 0.7913 (t80) REVERT: B 40 ASN cc_start: 0.8630 (t0) cc_final: 0.8364 (t0) REVERT: B 101 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8597 (tt) REVERT: B 171 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8261 (t80) REVERT: B 385 SER cc_start: 0.8211 (t) cc_final: 0.7691 (p) REVERT: B 531 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.7739 (m-70) REVERT: B 570 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7586 (t80) REVERT: B 573 SER cc_start: 0.9377 (t) cc_final: 0.8959 (m) REVERT: B 581 ILE cc_start: 0.9109 (tt) cc_final: 0.8908 (tt) REVERT: B 641 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.5633 (m-80) REVERT: B 682 GLN cc_start: 0.8693 (pm20) cc_final: 0.8392 (mt0) REVERT: B 690 PHE cc_start: 0.8261 (t80) cc_final: 0.7907 (t80) outliers start: 65 outliers final: 48 residues processed: 235 average time/residue: 0.1910 time to fit residues: 66.4238 Evaluate side-chains 238 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 191 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 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 107 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 191 GLN 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 478 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 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 660 CYS Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 115 optimal weight: 0.0020 chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN A 476 ASN ** A 670 HIS ** 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** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.142308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.111826 restraints weight = 17577.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115384 restraints weight = 7654.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.117611 restraints weight = 4754.030| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.6467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10906 Z= 0.158 Angle : 0.773 9.046 14824 Z= 0.388 Chirality : 0.044 0.206 1722 Planarity : 0.006 0.061 1808 Dihedral : 7.678 58.683 1458 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.34 % Favored : 88.36 % Rotamer: Outliers : 5.90 % Allowed : 31.68 % Favored : 62.41 % 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: -0.64 (0.25), residues: 1314 helix: 0.86 (0.18), residues: 902 sheet: -4.22 (0.92), residues: 20 loop : -3.38 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 240 HIS 0.002 0.001 HIS A 670 PHE 0.020 0.001 PHE A 465 TYR 0.022 0.001 TYR B 572 ARG 0.003 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 640) hydrogen bonds : angle 4.94876 ( 1872) covalent geometry : bond 0.00337 (10906) covalent geometry : angle 0.77331 (14824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 189 time to evaluate : 1.168 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 40 ASN cc_start: 0.8583 (t0) cc_final: 0.8318 (t0) REVERT: A 101 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8655 (tt) REVERT: A 171 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.8245 (t80) REVERT: A 177 LEU cc_start: 0.8625 (tt) cc_final: 0.8421 (tt) REVERT: A 385 SER cc_start: 0.8413 (t) cc_final: 0.8006 (p) REVERT: A 431 LYS cc_start: 0.8021 (tmtt) cc_final: 0.7344 (mptt) REVERT: A 570 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7291 (t80) REVERT: A 573 SER cc_start: 0.9368 (t) cc_final: 0.8920 (m) REVERT: A 641 PHE cc_start: 0.5959 (OUTLIER) cc_final: 0.5367 (m-80) REVERT: A 690 PHE cc_start: 0.8281 (t80) cc_final: 0.7799 (t80) REVERT: B 40 ASN cc_start: 0.8611 (t0) cc_final: 0.8363 (t0) REVERT: B 101 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8639 (tt) REVERT: B 171 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8242 (t80) REVERT: B 177 LEU cc_start: 0.8615 (tt) cc_final: 0.8406 (tt) REVERT: B 385 SER cc_start: 0.8136 (t) cc_final: 0.7593 (p) REVERT: B 431 LYS cc_start: 0.8038 (tmtt) cc_final: 0.7360 (mptt) REVERT: B 570 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7695 (t80) REVERT: B 573 SER cc_start: 0.9341 (t) cc_final: 0.8936 (m) REVERT: B 581 ILE cc_start: 0.9015 (tt) cc_final: 0.8776 (tt) REVERT: B 641 PHE cc_start: 0.5928 (OUTLIER) cc_final: 0.5289 (m-80) REVERT: B 682 GLN cc_start: 0.8688 (pm20) cc_final: 0.8326 (mt0) REVERT: B 690 PHE cc_start: 0.8274 (t80) cc_final: 0.7797 (t80) outliers start: 68 outliers final: 49 residues processed: 237 average time/residue: 0.1940 time to fit residues: 67.5002 Evaluate side-chains 236 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 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 183 MET Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 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 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 101 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 191 GLN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 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 567 THR Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 HIS ** A 670 HIS ** 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 326 GLN ** 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 531 HIS ** B 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.140876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.111799 restraints weight = 17279.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115165 restraints weight = 7477.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117271 restraints weight = 4587.580| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.6493 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= 0.168 Angle : 0.774 9.393 14824 Z= 0.388 Chirality : 0.045 0.205 1722 Planarity : 0.006 0.061 1808 Dihedral : 7.648 58.558 1458 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.34 % Favored : 88.36 % Rotamer: Outliers : 5.21 % Allowed : 32.29 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1314 helix: 0.85 (0.18), residues: 904 sheet: -3.84 (1.00), residues: 20 loop : -3.37 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 240 HIS 0.003 0.001 HIS B 670 PHE 0.024 0.001 PHE A 465 TYR 0.015 0.001 TYR A 572 ARG 0.003 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 640) hydrogen bonds : angle 4.95079 ( 1872) covalent geometry : bond 0.00372 (10906) covalent geometry : angle 0.77391 (14824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5246.94 seconds wall clock time: 94 minutes 51.94 seconds (5691.94 seconds total)