Starting phenix.real_space_refine on Thu Feb 15 11:08:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8g_15913/02_2024/8b8g_15913.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8g_15913/02_2024/8b8g_15913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8g_15913/02_2024/8b8g_15913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8g_15913/02_2024/8b8g_15913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8g_15913/02_2024/8b8g_15913.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8g_15913/02_2024/8b8g_15913.pdb" } resolution = 3.39 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= 0.017 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 80 5.16 5 C 7946 2.51 5 N 1944 2.21 5 O 2116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 624": "OE1" <-> "OE2" Residue "B PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6043 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 34, 'TRANS': 697} Chain breaks: 6 Chain: "B" Number of atoms: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6043 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 34, 'TRANS': 697} Chain breaks: 6 Time building chain proxies: 6.34, per 1000 atoms: 0.52 Number of scatterers: 12086 At special positions: 0 Unit cell: (119.784, 89.838, 119.784, 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 80 16.00 O 2116 8.00 N 1944 7.00 C 7946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.02 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.87 Conformation dependent library (CDL) restraints added in 2.1 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 64.1% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 91 through 109 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.742A pdb=" N PHE A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 294 through 327 Processing helix chain 'A' and resid 331 through 338 removed outlier: 3.919A pdb=" N LYS A 335 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.541A pdb=" N GLN A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.732A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.561A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 Processing helix chain 'A' and resid 448 through 489 removed outlier: 3.748A pdb=" N THR A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.970A pdb=" N LYS A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 572 removed outlier: 4.107A pdb=" N ILE A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 636 Proline residue: A 628 - end of helix removed outlier: 3.595A pdb=" N GLY A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.502A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.877A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 685 Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.524A pdb=" N LEU A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 3.916A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 759 Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.828A pdb=" N LEU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 877 Processing helix chain 'B' and resid 91 through 109 Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.742A pdb=" N PHE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 284 through 291 Processing helix chain 'B' and resid 294 through 327 Processing helix chain 'B' and resid 331 through 338 removed outlier: 3.919A pdb=" N LYS B 335 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.541A pdb=" N GLN B 345 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 342 through 346' Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.732A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.561A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 Processing helix chain 'B' and resid 448 through 489 removed outlier: 3.748A pdb=" N THR B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.970A pdb=" N LYS B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 572 removed outlier: 4.106A pdb=" N ILE B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 636 Proline residue: B 628 - end of helix removed outlier: 3.595A pdb=" N GLY B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG B 636 " --> pdb=" O ASN B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.503A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.877A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.524A pdb=" N LEU B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.916A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.828A pdb=" N LEU B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 877 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 116 Processing sheet with id=AA4, first strand: chain 'B' and resid 784 through 785 720 hydrogen bonds defined for protein. 2130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 5.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3688 1.34 - 1.46: 2730 1.46 - 1.57: 5884 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 12422 Sorted by residual: bond pdb=" N TYR B 564 " pdb=" CA TYR B 564 " ideal model delta sigma weight residual 1.457 1.443 0.014 1.33e-02 5.65e+03 1.14e+00 bond pdb=" N TYR A 564 " pdb=" CA TYR A 564 " ideal model delta sigma weight residual 1.457 1.443 0.014 1.33e-02 5.65e+03 1.06e+00 bond pdb=" C ASN B 562 " pdb=" O ASN B 562 " ideal model delta sigma weight residual 1.235 1.247 -0.012 1.26e-02 6.30e+03 8.85e-01 bond pdb=" C ASN A 562 " pdb=" O ASN A 562 " ideal model delta sigma weight residual 1.235 1.247 -0.012 1.26e-02 6.30e+03 8.62e-01 bond pdb=" CA ASN A 796 " pdb=" C ASN A 796 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 8.30e-01 ... (remaining 12417 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.70: 366 106.70 - 113.53: 6706 113.53 - 120.35: 4789 120.35 - 127.17: 4852 127.17 - 133.99: 139 Bond angle restraints: 16852 Sorted by residual: angle pdb=" C ALA A 245 " pdb=" N PHE A 246 " pdb=" CA PHE A 246 " ideal model delta sigma weight residual 123.15 112.47 10.68 2.23e+00 2.01e-01 2.29e+01 angle pdb=" C ALA B 245 " pdb=" N PHE B 246 " pdb=" CA PHE B 246 " ideal model delta sigma weight residual 123.15 112.49 10.66 2.23e+00 2.01e-01 2.29e+01 angle pdb=" N ILE B 233 " pdb=" CA ILE B 233 " pdb=" C ILE B 233 " ideal model delta sigma weight residual 111.90 108.85 3.05 8.10e-01 1.52e+00 1.42e+01 angle pdb=" N ILE A 233 " pdb=" CA ILE A 233 " pdb=" C ILE A 233 " ideal model delta sigma weight residual 111.90 108.86 3.04 8.10e-01 1.52e+00 1.41e+01 angle pdb=" N ILE A 279 " pdb=" CA ILE A 279 " pdb=" C ILE A 279 " ideal model delta sigma weight residual 112.96 109.40 3.56 1.00e+00 1.00e+00 1.27e+01 ... (remaining 16847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6723 17.67 - 35.33: 419 35.33 - 53.00: 130 53.00 - 70.67: 34 70.67 - 88.34: 10 Dihedral angle restraints: 7316 sinusoidal: 2982 harmonic: 4334 Sorted by residual: dihedral pdb=" CB CYS B 338 " pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " pdb=" CB CYS B 365 " ideal model delta sinusoidal sigma weight residual 93.00 58.42 34.58 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual 93.00 58.46 34.54 1 1.00e+01 1.00e-02 1.69e+01 dihedral pdb=" CA TYR A 222 " pdb=" C TYR A 222 " pdb=" N GLN A 223 " pdb=" CA GLN A 223 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1130 0.032 - 0.063: 512 0.063 - 0.095: 141 0.095 - 0.127: 51 0.127 - 0.158: 2 Chirality restraints: 1836 Sorted by residual: chirality pdb=" CA ILE A 762 " pdb=" N ILE A 762 " pdb=" C ILE A 762 " pdb=" CB ILE A 762 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE B 762 " pdb=" N ILE B 762 " pdb=" C ILE B 762 " pdb=" CB ILE B 762 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA PRO A 686 " pdb=" N PRO A 686 " pdb=" C PRO A 686 " pdb=" CB PRO A 686 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 1833 not shown) Planarity restraints: 2098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 763 " 0.043 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO A 764 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 764 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 764 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 763 " -0.043 5.00e-02 4.00e+02 6.40e-02 6.54e+00 pdb=" N PRO B 764 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 762 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO B 763 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 763 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 763 " 0.029 5.00e-02 4.00e+02 ... (remaining 2095 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 187 2.66 - 3.22: 12430 3.22 - 3.78: 19830 3.78 - 4.34: 24482 4.34 - 4.90: 40402 Nonbonded interactions: 97331 Sorted by model distance: nonbonded pdb=" OG1 THR A 307 " pdb=" OD1 ASN A 696 " model vdw 2.096 2.440 nonbonded pdb=" OG1 THR B 307 " pdb=" OD1 ASN B 696 " model vdw 2.097 2.440 nonbonded pdb=" O ILE A 744 " pdb=" OG SER A 748 " model vdw 2.162 2.440 nonbonded pdb=" O ILE B 744 " pdb=" OG SER B 748 " model vdw 2.162 2.440 nonbonded pdb=" O ALA B 571 " pdb=" OG1 THR B 747 " model vdw 2.174 2.440 ... (remaining 97326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 4.410 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 32.730 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.004 0.032 12422 Z= 0.271 Angle : 0.556 10.682 16852 Z= 0.310 Chirality : 0.040 0.158 1836 Planarity : 0.005 0.064 2098 Dihedral : 13.754 88.336 4510 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 7.59 % Allowed : 11.53 % Favored : 80.88 % 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: 0.87 (0.23), residues: 1436 helix: 1.72 (0.17), residues: 880 sheet: -2.17 (0.52), residues: 76 loop : -1.10 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS B 249 PHE 0.014 0.001 PHE B 560 TYR 0.015 0.001 TYR B 306 ARG 0.002 0.000 ARG B 808 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 183 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: A 243 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.8724 (tppp) REVERT: A 385 PHE cc_start: 0.9255 (t80) cc_final: 0.8999 (t80) REVERT: A 404 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8365 (mm) REVERT: A 405 GLU cc_start: 0.9410 (tm-30) cc_final: 0.9175 (tm-30) REVERT: A 417 GLU cc_start: 0.8950 (tp30) cc_final: 0.8592 (tp30) REVERT: A 533 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8756 (mp) REVERT: A 534 MET cc_start: 0.8164 (mpt) cc_final: 0.7723 (mpt) REVERT: A 557 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8351 (mm) REVERT: A 657 GLN cc_start: 0.8902 (mp-120) cc_final: 0.8627 (mp10) REVERT: A 661 LYS cc_start: 0.8722 (mtpp) cc_final: 0.8476 (mtpp) REVERT: A 717 GLU cc_start: 0.8440 (mp0) cc_final: 0.8229 (mp0) REVERT: A 721 ASP cc_start: 0.8589 (p0) cc_final: 0.8340 (p0) REVERT: B 125 PHE cc_start: 0.8767 (m-80) cc_final: 0.8398 (m-10) REVERT: B 145 LYS cc_start: 0.4150 (OUTLIER) cc_final: 0.3887 (tppt) REVERT: B 233 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8493 (tp) REVERT: B 371 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8917 (tt) REVERT: B 417 GLU cc_start: 0.8977 (tp30) cc_final: 0.8527 (tp30) REVERT: B 462 PHE cc_start: 0.8700 (t80) cc_final: 0.8447 (t80) REVERT: B 555 MET cc_start: 0.9006 (mmm) cc_final: 0.8716 (mmt) REVERT: B 557 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8386 (mt) REVERT: B 671 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.8677 (mpm) REVERT: B 721 ASP cc_start: 0.8552 (p0) cc_final: 0.8274 (p0) outliers start: 100 outliers final: 28 residues processed: 269 average time/residue: 0.2248 time to fit residues: 87.8997 Evaluate side-chains 161 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 823 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN A 710 GLN A 720 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN B 710 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12422 Z= 0.238 Angle : 0.579 11.592 16852 Z= 0.300 Chirality : 0.040 0.158 1836 Planarity : 0.005 0.066 2098 Dihedral : 8.586 84.552 1699 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.01 % Allowed : 16.54 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.22), residues: 1436 helix: 1.91 (0.17), residues: 882 sheet: -2.13 (0.53), residues: 76 loop : -0.87 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS B 143 PHE 0.020 0.001 PHE B 852 TYR 0.014 0.002 TYR A 563 ARG 0.002 0.000 ARG B 649 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 136 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.7870 (mpt180) cc_final: 0.7435 (mpt180) REVERT: A 385 PHE cc_start: 0.9255 (t80) cc_final: 0.9026 (t80) REVERT: A 404 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8265 (mm) REVERT: A 409 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8200 (t0) REVERT: A 417 GLU cc_start: 0.8954 (tp30) cc_final: 0.8479 (tp30) REVERT: A 534 MET cc_start: 0.8087 (mpt) cc_final: 0.7526 (mpt) REVERT: A 557 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8260 (mt) REVERT: A 661 LYS cc_start: 0.8686 (mtpp) cc_final: 0.8320 (mtpp) REVERT: B 125 PHE cc_start: 0.8801 (m-80) cc_final: 0.8472 (m-10) REVERT: B 371 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8840 (tt) REVERT: B 417 GLU cc_start: 0.8964 (tp30) cc_final: 0.8483 (tp30) REVERT: B 462 PHE cc_start: 0.8666 (t80) cc_final: 0.8461 (t80) REVERT: B 489 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6666 (mt) REVERT: B 555 MET cc_start: 0.9050 (mmm) cc_final: 0.8781 (mmt) REVERT: B 557 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8386 (mt) REVERT: B 671 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.8424 (mpm) outliers start: 66 outliers final: 40 residues processed: 192 average time/residue: 0.2138 time to fit residues: 61.9563 Evaluate side-chains 161 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 114 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 0.0970 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 131 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12422 Z= 0.185 Angle : 0.529 9.895 16852 Z= 0.277 Chirality : 0.040 0.169 1836 Planarity : 0.005 0.066 2098 Dihedral : 7.716 79.971 1678 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.93 % Allowed : 17.00 % Favored : 78.07 % 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: 1.26 (0.22), residues: 1436 helix: 2.04 (0.17), residues: 880 sheet: -2.18 (0.52), residues: 76 loop : -0.92 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 397 HIS 0.002 0.000 HIS B 143 PHE 0.020 0.001 PHE B 852 TYR 0.015 0.001 TYR B 305 ARG 0.002 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 136 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.7889 (mpt180) cc_final: 0.7338 (mpt180) REVERT: A 255 TYR cc_start: 0.6981 (m-80) cc_final: 0.6762 (m-80) REVERT: A 385 PHE cc_start: 0.9250 (t80) cc_final: 0.9044 (t80) REVERT: A 404 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8384 (mm) REVERT: A 409 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8191 (t0) REVERT: A 417 GLU cc_start: 0.8923 (tp30) cc_final: 0.8571 (tp30) REVERT: A 516 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8470 (pp) REVERT: A 533 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8821 (mp) REVERT: A 534 MET cc_start: 0.8052 (mpt) cc_final: 0.7542 (mpt) REVERT: A 557 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8237 (mt) REVERT: A 661 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8356 (mtpp) REVERT: B 145 LYS cc_start: 0.4169 (OUTLIER) cc_final: 0.3869 (tppt) REVERT: B 371 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8757 (tt) REVERT: B 409 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8034 (t0) REVERT: B 489 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6401 (mt) REVERT: B 555 MET cc_start: 0.9094 (mmm) cc_final: 0.8824 (mmt) REVERT: B 557 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8416 (mt) outliers start: 65 outliers final: 37 residues processed: 190 average time/residue: 0.2177 time to fit residues: 63.0258 Evaluate side-chains 164 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 117 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 0.0040 chunk 68 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12422 Z= 0.176 Angle : 0.512 9.067 16852 Z= 0.271 Chirality : 0.039 0.157 1836 Planarity : 0.005 0.066 2098 Dihedral : 7.483 80.547 1673 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.86 % Allowed : 18.29 % Favored : 76.86 % 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: 1.34 (0.22), residues: 1436 helix: 2.11 (0.17), residues: 878 sheet: -2.22 (0.51), residues: 76 loop : -0.89 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 397 HIS 0.002 0.000 HIS B 143 PHE 0.020 0.001 PHE B 852 TYR 0.014 0.001 TYR A 306 ARG 0.001 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 128 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.7018 (m-80) cc_final: 0.6780 (m-80) REVERT: A 385 PHE cc_start: 0.9239 (t80) cc_final: 0.9034 (t80) REVERT: A 404 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8401 (mm) REVERT: A 409 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8196 (t0) REVERT: A 417 GLU cc_start: 0.8906 (tp30) cc_final: 0.8524 (tp30) REVERT: A 534 MET cc_start: 0.8046 (mpt) cc_final: 0.7537 (mpt) REVERT: A 556 PHE cc_start: 0.9253 (t80) cc_final: 0.9026 (t80) REVERT: A 557 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8186 (mm) REVERT: A 631 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8098 (mpt) REVERT: A 661 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8271 (mtpp) REVERT: A 721 ASP cc_start: 0.8307 (p0) cc_final: 0.7848 (t0) REVERT: B 371 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8867 (tt) REVERT: B 409 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.7987 (t0) REVERT: B 489 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6453 (mt) REVERT: B 555 MET cc_start: 0.9104 (mmm) cc_final: 0.8841 (mmt) REVERT: B 557 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8381 (mt) REVERT: B 670 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8313 (tm-30) outliers start: 64 outliers final: 41 residues processed: 175 average time/residue: 0.2118 time to fit residues: 56.4311 Evaluate side-chains 166 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 117 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN B 254 ASN B 345 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12422 Z= 0.271 Angle : 0.557 9.090 16852 Z= 0.295 Chirality : 0.041 0.168 1836 Planarity : 0.005 0.065 2098 Dihedral : 7.380 80.169 1666 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.77 % Allowed : 19.04 % Favored : 75.19 % 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: 1.22 (0.22), residues: 1436 helix: 1.99 (0.17), residues: 886 sheet: -2.27 (0.51), residues: 76 loop : -0.94 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.003 0.001 HIS A 249 PHE 0.022 0.002 PHE B 852 TYR 0.019 0.002 TYR A 306 ARG 0.003 0.000 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 121 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8931 (tt) REVERT: A 404 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8379 (mm) REVERT: A 409 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8126 (t0) REVERT: A 417 GLU cc_start: 0.8930 (tp30) cc_final: 0.8535 (tp30) REVERT: A 534 MET cc_start: 0.8115 (mpt) cc_final: 0.7661 (mpt) REVERT: A 557 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8269 (mm) REVERT: A 631 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7956 (mpt) REVERT: A 661 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8439 (mtpp) REVERT: B 113 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7005 (pm20) REVERT: B 371 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8860 (tt) REVERT: B 409 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.7998 (t0) REVERT: B 489 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6529 (mt) REVERT: B 555 MET cc_start: 0.9093 (mmm) cc_final: 0.8828 (mmt) REVERT: B 557 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8403 (mm) REVERT: B 601 CYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8187 (m) outliers start: 76 outliers final: 52 residues processed: 177 average time/residue: 0.2173 time to fit residues: 57.7296 Evaluate side-chains 176 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 113 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A 608 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12422 Z= 0.183 Angle : 0.516 8.012 16852 Z= 0.275 Chirality : 0.040 0.156 1836 Planarity : 0.005 0.066 2098 Dihedral : 7.275 80.637 1665 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.01 % Allowed : 20.86 % Favored : 74.13 % 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: 1.28 (0.22), residues: 1436 helix: 2.06 (0.17), residues: 884 sheet: -2.28 (0.51), residues: 76 loop : -0.95 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.002 0.000 HIS B 143 PHE 0.028 0.001 PHE A 385 TYR 0.013 0.001 TYR A 569 ARG 0.001 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 133 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8757 (tt) REVERT: A 404 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8386 (mm) REVERT: A 409 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8133 (t0) REVERT: A 417 GLU cc_start: 0.8919 (tp30) cc_final: 0.8523 (tp30) REVERT: A 534 MET cc_start: 0.8091 (mpt) cc_final: 0.7652 (mpt) REVERT: A 556 PHE cc_start: 0.9239 (t80) cc_final: 0.8970 (t80) REVERT: A 557 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8187 (mm) REVERT: A 631 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7937 (mpt) REVERT: A 657 GLN cc_start: 0.9014 (mp10) cc_final: 0.8743 (mp10) REVERT: A 661 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8399 (mtpp) REVERT: A 721 ASP cc_start: 0.8192 (p0) cc_final: 0.7801 (t0) REVERT: B 113 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7041 (pm20) REVERT: B 371 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8968 (tt) REVERT: B 409 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.7976 (t0) REVERT: B 489 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6435 (mt) REVERT: B 555 MET cc_start: 0.9035 (mmm) cc_final: 0.8734 (mmt) REVERT: B 557 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8324 (mm) REVERT: B 601 CYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8221 (m) REVERT: B 609 LEU cc_start: 0.9549 (tt) cc_final: 0.9227 (tt) REVERT: B 671 MET cc_start: 0.9491 (tpp) cc_final: 0.9220 (mmt) outliers start: 66 outliers final: 44 residues processed: 182 average time/residue: 0.2326 time to fit residues: 62.8855 Evaluate side-chains 176 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 121 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 85 optimal weight: 0.0070 chunk 64 optimal weight: 0.2980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12422 Z= 0.154 Angle : 0.506 7.203 16852 Z= 0.267 Chirality : 0.040 0.207 1836 Planarity : 0.005 0.066 2098 Dihedral : 7.200 81.027 1665 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.17 % Allowed : 21.93 % Favored : 73.90 % 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: 1.37 (0.22), residues: 1436 helix: 2.14 (0.17), residues: 884 sheet: -2.22 (0.50), residues: 76 loop : -0.93 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 389 HIS 0.002 0.000 HIS B 143 PHE 0.027 0.001 PHE B 385 TYR 0.015 0.001 TYR A 306 ARG 0.001 0.000 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 136 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.5981 (tpt) cc_final: 0.5021 (pmm) REVERT: A 306 TYR cc_start: 0.9260 (t80) cc_final: 0.8966 (t80) REVERT: A 371 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8751 (tt) REVERT: A 409 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8079 (t0) REVERT: A 417 GLU cc_start: 0.8886 (tp30) cc_final: 0.8468 (tp30) REVERT: A 534 MET cc_start: 0.8060 (mpt) cc_final: 0.7650 (mpt) REVERT: A 556 PHE cc_start: 0.9208 (t80) cc_final: 0.8928 (t80) REVERT: A 557 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8169 (mm) REVERT: A 609 LEU cc_start: 0.9446 (tt) cc_final: 0.9243 (tt) REVERT: A 631 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8151 (mpt) REVERT: A 661 LYS cc_start: 0.8703 (mtpp) cc_final: 0.8441 (mtpp) REVERT: A 721 ASP cc_start: 0.8190 (p0) cc_final: 0.7823 (t0) REVERT: B 371 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8979 (tt) REVERT: B 409 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.7961 (t0) REVERT: B 489 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6403 (mt) REVERT: B 555 MET cc_start: 0.8961 (mmm) cc_final: 0.8647 (mmt) REVERT: B 557 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8277 (mm) REVERT: B 601 CYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8189 (m) REVERT: B 609 LEU cc_start: 0.9547 (tt) cc_final: 0.9206 (tt) REVERT: B 671 MET cc_start: 0.9431 (tpp) cc_final: 0.9197 (mmp) outliers start: 55 outliers final: 37 residues processed: 173 average time/residue: 0.2121 time to fit residues: 55.1617 Evaluate side-chains 175 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 129 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 95 optimal weight: 0.0670 chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12422 Z= 0.161 Angle : 0.508 6.699 16852 Z= 0.268 Chirality : 0.040 0.211 1836 Planarity : 0.005 0.067 2098 Dihedral : 6.677 81.518 1657 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.32 % Allowed : 22.00 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.22), residues: 1436 helix: 2.14 (0.17), residues: 894 sheet: -2.08 (0.52), residues: 66 loop : -1.01 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 389 HIS 0.002 0.000 HIS B 143 PHE 0.028 0.001 PHE B 385 TYR 0.015 0.001 TYR A 306 ARG 0.001 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 131 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.5988 (tpt) cc_final: 0.5274 (pmm) REVERT: A 371 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8747 (tt) REVERT: A 409 ASP cc_start: 0.9083 (OUTLIER) cc_final: 0.8208 (t0) REVERT: A 417 GLU cc_start: 0.8872 (tp30) cc_final: 0.8456 (tp30) REVERT: A 534 MET cc_start: 0.8008 (mpt) cc_final: 0.7569 (mpt) REVERT: A 556 PHE cc_start: 0.9226 (t80) cc_final: 0.8968 (t80) REVERT: A 557 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8180 (mm) REVERT: A 609 LEU cc_start: 0.9446 (tt) cc_final: 0.9230 (tt) REVERT: A 631 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8110 (mpt) REVERT: A 661 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8381 (mtpp) REVERT: A 721 ASP cc_start: 0.8182 (p0) cc_final: 0.7831 (t0) REVERT: A 842 MET cc_start: 0.8792 (tmm) cc_final: 0.8585 (tmm) REVERT: B 371 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9091 (tt) REVERT: B 409 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8020 (t0) REVERT: B 555 MET cc_start: 0.8961 (mmm) cc_final: 0.8648 (mmt) REVERT: B 557 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8257 (mm) REVERT: B 601 CYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8182 (m) REVERT: B 609 LEU cc_start: 0.9543 (tt) cc_final: 0.9209 (tt) REVERT: B 671 MET cc_start: 0.9410 (tpp) cc_final: 0.9151 (mmt) outliers start: 57 outliers final: 41 residues processed: 170 average time/residue: 0.2135 time to fit residues: 54.4966 Evaluate side-chains 178 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 129 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 57 optimal weight: 0.0020 chunk 102 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 130 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12422 Z= 0.150 Angle : 0.504 7.012 16852 Z= 0.266 Chirality : 0.040 0.214 1836 Planarity : 0.005 0.067 2098 Dihedral : 6.170 58.893 1654 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.17 % Allowed : 22.46 % Favored : 73.37 % 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: 1.42 (0.22), residues: 1436 helix: 2.15 (0.17), residues: 896 sheet: -2.10 (0.52), residues: 66 loop : -0.99 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 389 HIS 0.002 0.000 HIS B 143 PHE 0.028 0.001 PHE B 385 TYR 0.014 0.001 TYR A 306 ARG 0.001 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 139 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.6258 (tpt) cc_final: 0.5576 (pmm) REVERT: A 371 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8745 (tt) REVERT: A 409 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8210 (t0) REVERT: A 417 GLU cc_start: 0.8870 (tp30) cc_final: 0.8491 (tp30) REVERT: A 534 MET cc_start: 0.7907 (mpt) cc_final: 0.7495 (mpt) REVERT: A 556 PHE cc_start: 0.9204 (t80) cc_final: 0.9003 (t80) REVERT: A 557 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8159 (mm) REVERT: A 609 LEU cc_start: 0.9442 (tt) cc_final: 0.9213 (tt) REVERT: A 631 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8142 (mpt) REVERT: A 661 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8381 (mtpp) REVERT: A 721 ASP cc_start: 0.8168 (p0) cc_final: 0.7863 (t0) REVERT: A 773 MET cc_start: 0.9261 (mmm) cc_final: 0.9049 (tpp) REVERT: B 371 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8974 (tt) REVERT: B 409 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8024 (t0) REVERT: B 555 MET cc_start: 0.8941 (mmm) cc_final: 0.8622 (mmt) REVERT: B 557 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8251 (mm) REVERT: B 601 CYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8160 (m) REVERT: B 609 LEU cc_start: 0.9532 (tt) cc_final: 0.9188 (tt) outliers start: 55 outliers final: 42 residues processed: 176 average time/residue: 0.2184 time to fit residues: 57.9125 Evaluate side-chains 178 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 128 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12422 Z= 0.162 Angle : 0.515 7.994 16852 Z= 0.271 Chirality : 0.040 0.215 1836 Planarity : 0.005 0.067 2098 Dihedral : 6.161 59.960 1654 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.02 % Allowed : 22.84 % Favored : 73.14 % 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: 1.42 (0.22), residues: 1436 helix: 2.21 (0.17), residues: 886 sheet: -2.09 (0.52), residues: 66 loop : -1.06 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 389 HIS 0.002 0.000 HIS B 143 PHE 0.035 0.001 PHE B 385 TYR 0.014 0.001 TYR A 569 ARG 0.001 0.000 ARG B 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 131 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.6249 (tpt) cc_final: 0.5529 (pmm) REVERT: A 288 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8495 (tp) REVERT: A 371 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8735 (tt) REVERT: A 409 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8234 (t0) REVERT: A 417 GLU cc_start: 0.8889 (tp30) cc_final: 0.8489 (tp30) REVERT: A 534 MET cc_start: 0.7891 (mpt) cc_final: 0.7506 (mpt) REVERT: A 557 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8146 (mm) REVERT: A 609 LEU cc_start: 0.9457 (tt) cc_final: 0.9177 (tt) REVERT: A 631 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8192 (mpt) REVERT: A 661 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8359 (mtpp) REVERT: A 721 ASP cc_start: 0.8155 (p0) cc_final: 0.7811 (t0) REVERT: B 371 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8970 (tt) REVERT: B 409 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8029 (t0) REVERT: B 555 MET cc_start: 0.8947 (mmm) cc_final: 0.8631 (mmt) REVERT: B 557 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8226 (mm) REVERT: B 601 CYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8170 (m) REVERT: B 609 LEU cc_start: 0.9533 (tt) cc_final: 0.9186 (tt) outliers start: 53 outliers final: 41 residues processed: 168 average time/residue: 0.2183 time to fit residues: 55.4566 Evaluate side-chains 177 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 127 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 TYR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 823 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 32 optimal weight: 0.0070 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 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 = 0.3643 r_free = 0.3643 target = 0.103684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.078835 restraints weight = 29182.947| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.48 r_work: 0.3031 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12422 Z= 0.151 Angle : 0.509 7.057 16852 Z= 0.268 Chirality : 0.040 0.209 1836 Planarity : 0.005 0.067 2098 Dihedral : 6.088 59.107 1654 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.79 % Allowed : 22.91 % Favored : 73.29 % 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: 1.45 (0.23), residues: 1436 helix: 2.22 (0.17), residues: 888 sheet: -2.03 (0.52), residues: 66 loop : -1.05 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 389 HIS 0.002 0.000 HIS B 143 PHE 0.033 0.001 PHE B 385 TYR 0.015 0.001 TYR B 569 ARG 0.001 0.000 ARG B 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2421.46 seconds wall clock time: 45 minutes 13.39 seconds (2713.39 seconds total)