Starting phenix.real_space_refine on Fri Mar 15 12:00:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grn_34209/03_2024/8grn_34209_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grn_34209/03_2024/8grn_34209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grn_34209/03_2024/8grn_34209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grn_34209/03_2024/8grn_34209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grn_34209/03_2024/8grn_34209_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grn_34209/03_2024/8grn_34209_neut_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.066 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 52 5.16 5 C 7648 2.51 5 N 1898 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "B GLU 558": "OE1" <-> "OE2" Residue "B GLU 571": "OE1" <-> "OE2" Residue "B GLU 617": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B ARG 671": "NH1" <-> "NH2" Residue "B GLU 678": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11602 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5770 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 37, 'TRANS': 678} Chain: "B" Number of atoms: 5770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5770 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 37, 'TRANS': 678} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LPC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LPC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.32, per 1000 atoms: 0.54 Number of scatterers: 11602 At special positions: 0 Unit cell: (153.669, 111.219, 106.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 2 15.00 O 2002 8.00 N 1898 7.00 C 7648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 4.50 Conformation dependent library (CDL) restraints added in 2.2 seconds 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 2 sheets defined 57.3% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 4 through 30 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 73 through 80 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 93 through 125 Proline residue: A 111 - end of helix Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 160 through 192 Processing helix chain 'A' and resid 221 through 228 removed outlier: 3.578A pdb=" N VAL A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 260 Processing helix chain 'A' and resid 292 through 315 Processing helix chain 'A' and resid 334 through 337 No H-bonds generated for 'chain 'A' and resid 334 through 337' Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 369 through 401 Proline residue: A 393 - end of helix removed outlier: 3.880A pdb=" N LEU A 400 " --> pdb=" O PHE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 450 removed outlier: 3.719A pdb=" N LEU A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 458 through 495 removed outlier: 3.657A pdb=" N GLU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 534 Proline residue: A 511 - end of helix removed outlier: 3.774A pdb=" N ILE A 533 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 547 removed outlier: 3.592A pdb=" N TYR A 542 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 585 Proline residue: A 572 - end of helix Processing helix chain 'A' and resid 592 through 611 Processing helix chain 'A' and resid 624 through 649 Processing helix chain 'A' and resid 656 through 682 Proline residue: A 663 - end of helix Proline residue: A 679 - end of helix Processing helix chain 'A' and resid 686 through 693 Processing helix chain 'A' and resid 705 through 710 removed outlier: 3.604A pdb=" N GLN A 710 " --> pdb=" O LYS A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 30 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 73 through 80 Proline residue: B 77 - end of helix Processing helix chain 'B' and resid 93 through 125 Proline residue: B 111 - end of helix Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 131 through 134 No H-bonds generated for 'chain 'B' and resid 131 through 134' Processing helix chain 'B' and resid 160 through 192 Processing helix chain 'B' and resid 221 through 228 removed outlier: 3.578A pdb=" N VAL B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 261 Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.751A pdb=" N SER B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 337 No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 369 through 401 Proline residue: B 393 - end of helix removed outlier: 3.880A pdb=" N LEU B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 450 removed outlier: 3.719A pdb=" N LEU B 425 " --> pdb=" O PHE B 421 " (cutoff:3.500A) Proline residue: B 443 - end of helix Processing helix chain 'B' and resid 458 through 495 removed outlier: 3.657A pdb=" N GLU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 534 Proline residue: B 511 - end of helix removed outlier: 3.774A pdb=" N ILE B 533 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 547 removed outlier: 3.592A pdb=" N TYR B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 585 Proline residue: B 572 - end of helix Processing helix chain 'B' and resid 592 through 611 Processing helix chain 'B' and resid 624 through 649 Processing helix chain 'B' and resid 656 through 682 Proline residue: B 663 - end of helix Proline residue: B 679 - end of helix Processing helix chain 'B' and resid 686 through 693 Processing helix chain 'B' and resid 705 through 710 removed outlier: 3.604A pdb=" N GLN B 710 " --> pdb=" O LYS B 706 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 203 through 207 removed outlier: 4.696A pdb=" N VAL A 239 " --> pdb=" O MET A 321 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA A 323 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN A 237 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A 325 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A 235 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 203 through 207 removed outlier: 4.696A pdb=" N VAL B 239 " --> pdb=" O MET B 321 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA B 323 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN B 237 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE B 325 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR B 235 " --> pdb=" O PHE B 325 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1499 1.25 - 1.39: 3422 1.39 - 1.53: 6426 1.53 - 1.67: 472 1.67 - 1.81: 97 Bond restraints: 11916 Sorted by residual: bond pdb=" C LEU B 437 " pdb=" O LEU B 437 " ideal model delta sigma weight residual 1.236 1.521 -0.285 1.16e-02 7.43e+03 6.04e+02 bond pdb=" C LEU A 437 " pdb=" O LEU A 437 " ideal model delta sigma weight residual 1.236 1.521 -0.285 1.16e-02 7.43e+03 6.04e+02 bond pdb=" C ALA A 623 " pdb=" O ALA A 623 " ideal model delta sigma weight residual 1.236 1.546 -0.309 1.32e-02 5.74e+03 5.49e+02 bond pdb=" C ALA B 623 " pdb=" O ALA B 623 " ideal model delta sigma weight residual 1.236 1.546 -0.309 1.32e-02 5.74e+03 5.49e+02 bond pdb=" C ILE B 440 " pdb=" O ILE B 440 " ideal model delta sigma weight residual 1.237 1.495 -0.259 1.12e-02 7.97e+03 5.34e+02 ... (remaining 11911 not shown) Histogram of bond angle deviations from ideal: 70.54 - 86.21: 9 86.21 - 101.88: 235 101.88 - 117.55: 7967 117.55 - 133.23: 7940 133.23 - 148.90: 45 Bond angle restraints: 16196 Sorted by residual: angle pdb=" N GLU A 298 " pdb=" CA GLU A 298 " pdb=" C GLU A 298 " ideal model delta sigma weight residual 111.69 70.54 41.15 1.23e+00 6.61e-01 1.12e+03 angle pdb=" C ALA B 585 " pdb=" N PRO B 586 " pdb=" CA PRO B 586 " ideal model delta sigma weight residual 120.83 99.27 21.56 1.02e+00 9.61e-01 4.47e+02 angle pdb=" C ALA A 585 " pdb=" N PRO A 586 " pdb=" CA PRO A 586 " ideal model delta sigma weight residual 120.83 99.27 21.56 1.02e+00 9.61e-01 4.47e+02 angle pdb=" N ASP A 316 " pdb=" CA ASP A 316 " pdb=" C ASP A 316 " ideal model delta sigma weight residual 112.92 138.48 -25.56 1.23e+00 6.61e-01 4.32e+02 angle pdb=" N LYS A 81 " pdb=" CA LYS A 81 " pdb=" C LYS A 81 " ideal model delta sigma weight residual 113.21 135.17 -21.96 1.15e+00 7.56e-01 3.65e+02 ... (remaining 16191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5490 17.88 - 35.76: 850 35.76 - 53.64: 542 53.64 - 71.52: 157 71.52 - 89.40: 17 Dihedral angle restraints: 7056 sinusoidal: 2842 harmonic: 4214 Sorted by residual: dihedral pdb=" C LEU B 259 " pdb=" N LEU B 259 " pdb=" CA LEU B 259 " pdb=" CB LEU B 259 " ideal model delta harmonic sigma weight residual -122.60 -159.94 37.34 0 2.50e+00 1.60e-01 2.23e+02 dihedral pdb=" N LEU B 259 " pdb=" C LEU B 259 " pdb=" CA LEU B 259 " pdb=" CB LEU B 259 " ideal model delta harmonic sigma weight residual 122.80 158.36 -35.56 0 2.50e+00 1.60e-01 2.02e+02 dihedral pdb=" C ASN A 568 " pdb=" N ASN A 568 " pdb=" CA ASN A 568 " pdb=" CB ASN A 568 " ideal model delta harmonic sigma weight residual -122.60 -153.57 30.97 0 2.50e+00 1.60e-01 1.53e+02 ... (remaining 7053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.337: 1510 0.337 - 0.674: 273 0.674 - 1.012: 29 1.012 - 1.349: 5 1.349 - 1.686: 1 Chirality restraints: 1818 Sorted by residual: chirality pdb=" CA LEU B 259 " pdb=" N LEU B 259 " pdb=" C LEU B 259 " pdb=" CB LEU B 259 " both_signs ideal model delta sigma weight residual False 2.51 0.82 1.69 2.00e-01 2.50e+01 7.10e+01 chirality pdb=" CA ASN A 568 " pdb=" N ASN A 568 " pdb=" C ASN A 568 " pdb=" CB ASN A 568 " both_signs ideal model delta sigma weight residual False 2.51 1.22 1.29 2.00e-01 2.50e+01 4.19e+01 chirality pdb=" CA ASN B 568 " pdb=" N ASN B 568 " pdb=" C ASN B 568 " pdb=" CB ASN B 568 " both_signs ideal model delta sigma weight residual False 2.51 1.22 1.29 2.00e-01 2.50e+01 4.19e+01 ... (remaining 1815 not shown) Planarity restraints: 2024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 240 " 0.055 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C CYS A 240 " -0.174 2.00e-02 2.50e+03 pdb=" O CYS A 240 " 0.064 2.00e-02 2.50e+03 pdb=" N ASN A 241 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 296 " 0.052 2.00e-02 2.50e+03 9.63e-02 9.27e+01 pdb=" C ILE A 296 " -0.167 2.00e-02 2.50e+03 pdb=" O ILE A 296 " 0.063 2.00e-02 2.50e+03 pdb=" N ALA A 297 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 499 " -0.046 2.00e-02 2.50e+03 8.53e-02 7.27e+01 pdb=" C PRO B 499 " 0.148 2.00e-02 2.50e+03 pdb=" O PRO B 499 " -0.052 2.00e-02 2.50e+03 pdb=" N ASN B 500 " -0.050 2.00e-02 2.50e+03 ... (remaining 2021 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.23: 22 2.23 - 2.90: 5488 2.90 - 3.57: 15856 3.57 - 4.23: 27500 4.23 - 4.90: 46021 Nonbonded interactions: 94887 Sorted by model distance: nonbonded pdb=" CD LYS B 554 " pdb=" NH1 ARG B 556 " model vdw 1.568 3.520 nonbonded pdb=" CD LYS A 554 " pdb=" NH1 ARG A 556 " model vdw 1.568 3.520 nonbonded pdb=" N GLU A 298 " pdb=" N VAL A 299 " model vdw 1.842 2.560 nonbonded pdb=" O TYR A 295 " pdb=" N ALA A 297 " model vdw 1.958 2.520 nonbonded pdb=" N ARG B 198 " pdb=" O ARG B 198 " model vdw 2.125 2.496 ... (remaining 94882 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: 3.690 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: 13.540 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.880 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 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 : 0.033 0.370 11916 Z= 2.077 Angle : 3.219 41.152 16196 Z= 2.122 Chirality : 0.257 1.686 1818 Planarity : 0.022 0.189 2024 Dihedral : 23.949 89.397 4328 Min Nonbonded Distance : 1.568 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 7.42 % Allowed : 14.78 % Favored : 77.80 % Rotamer: Outliers : 36.57 % Allowed : 16.18 % Favored : 47.25 % Cbeta Deviations : 12.98 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.62 (0.16), residues: 1428 helix: -3.22 (0.12), residues: 900 sheet: -2.13 (0.68), residues: 44 loop : -4.65 (0.22), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP B 75 HIS 0.015 0.004 HIS B 236 PHE 0.047 0.005 PHE B 624 TYR 0.035 0.004 TYR B 618 ARG 0.006 0.001 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 452 poor density : 183 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.5734 (OUTLIER) cc_final: 0.5523 (tttm) REVERT: A 76 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6853 (mtt) REVERT: A 115 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6737 (mt) REVERT: A 122 PRO cc_start: 0.6814 (OUTLIER) cc_final: 0.6109 (Cg_exo) REVERT: A 178 MET cc_start: 0.6288 (ttp) cc_final: 0.6080 (ttp) REVERT: A 205 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8250 (tp) REVERT: A 212 ASP cc_start: 0.6090 (OUTLIER) cc_final: 0.5873 (t70) REVERT: A 278 LYS cc_start: 0.3059 (OUTLIER) cc_final: 0.1568 (ttpt) REVERT: A 301 LYS cc_start: 0.5522 (OUTLIER) cc_final: 0.5249 (ptmt) REVERT: A 370 VAL cc_start: 0.5164 (OUTLIER) cc_final: 0.4871 (m) REVERT: A 379 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6850 (mmp) REVERT: A 394 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.5982 (mp) REVERT: A 400 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7748 (mp) REVERT: A 457 SER cc_start: 0.7703 (OUTLIER) cc_final: 0.7179 (p) REVERT: A 491 LEU cc_start: 0.5553 (OUTLIER) cc_final: 0.4473 (tp) REVERT: A 572 PRO cc_start: 0.7827 (OUTLIER) cc_final: 0.7416 (Cg_exo) REVERT: A 590 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.6226 (ttt) REVERT: A 659 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6686 (mt) REVERT: A 660 ILE cc_start: 0.6213 (OUTLIER) cc_final: 0.5967 (mp) REVERT: A 709 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8126 (mt) REVERT: B 5 LYS cc_start: 0.5733 (OUTLIER) cc_final: 0.5521 (tttm) REVERT: B 76 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6854 (mtt) REVERT: B 115 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6737 (mt) REVERT: B 122 PRO cc_start: 0.6813 (OUTLIER) cc_final: 0.6111 (Cg_exo) REVERT: B 178 MET cc_start: 0.6292 (ttp) cc_final: 0.6079 (ttp) REVERT: B 205 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8255 (tp) REVERT: B 212 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5872 (t70) REVERT: B 278 LYS cc_start: 0.3081 (OUTLIER) cc_final: 0.1501 (ttpt) REVERT: B 294 HIS cc_start: 0.5879 (OUTLIER) cc_final: 0.5074 (m90) REVERT: B 370 VAL cc_start: 0.5163 (OUTLIER) cc_final: 0.4871 (m) REVERT: B 379 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6857 (mmp) REVERT: B 394 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.5986 (mp) REVERT: B 400 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7731 (mp) REVERT: B 457 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7180 (p) REVERT: B 491 LEU cc_start: 0.5553 (OUTLIER) cc_final: 0.4464 (tp) REVERT: B 572 PRO cc_start: 0.7830 (OUTLIER) cc_final: 0.7418 (Cg_exo) REVERT: B 590 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.6235 (ttt) REVERT: B 659 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6687 (mt) REVERT: B 660 ILE cc_start: 0.6210 (OUTLIER) cc_final: 0.5965 (mp) REVERT: B 709 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8127 (mt) outliers start: 452 outliers final: 134 residues processed: 560 average time/residue: 0.9807 time to fit residues: 603.0809 Evaluate side-chains 325 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 153 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 111 PRO Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 122 PRO Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 503 PRO Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 572 PRO Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 111 PRO Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 122 PRO Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 503 PRO Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 556 ARG Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 572 PRO Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 616 GLN Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 699 ARG Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 74 HIS A 90 HIS A 124 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN A 476 ASN A 490 GLN A 497 GLN A 500 ASN A 543 HIS A 546 ASN A 568 ASN A 573 GLN A 575 GLN A 616 GLN A 687 GLN B 63 ASN B 74 HIS B 90 HIS B 124 ASN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN B 476 ASN B 490 GLN B 497 GLN B 500 ASN B 543 HIS B 546 ASN B 568 ASN B 573 GLN B 575 GLN B 616 GLN B 687 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 11916 Z= 0.304 Angle : 0.970 14.695 16196 Z= 0.513 Chirality : 0.056 0.322 1818 Planarity : 0.009 0.098 2024 Dihedral : 15.567 74.428 1980 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 1.47 % Allowed : 11.41 % Favored : 87.11 % Rotamer: Outliers : 11.57 % Allowed : 26.05 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.21), residues: 1428 helix: -0.47 (0.17), residues: 870 sheet: -3.51 (0.54), residues: 46 loop : -4.32 (0.21), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 75 HIS 0.005 0.001 HIS B 715 PHE 0.023 0.002 PHE B 136 TYR 0.022 0.002 TYR A 98 ARG 0.011 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 178 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.5249 (OUTLIER) cc_final: 0.5021 (tptp) REVERT: A 50 SER cc_start: 0.5386 (OUTLIER) cc_final: 0.4917 (m) REVERT: A 178 MET cc_start: 0.5844 (ttp) cc_final: 0.5642 (ttp) REVERT: A 212 ASP cc_start: 0.5804 (OUTLIER) cc_final: 0.5532 (t70) REVERT: A 295 TYR cc_start: 0.3074 (OUTLIER) cc_final: 0.2870 (m-80) REVERT: A 379 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6965 (mmp) REVERT: A 439 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.5988 (mt) REVERT: A 457 SER cc_start: 0.7399 (OUTLIER) cc_final: 0.7055 (p) REVERT: A 491 LEU cc_start: 0.3825 (OUTLIER) cc_final: 0.2421 (tt) REVERT: A 590 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5987 (ttt) REVERT: A 659 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7700 (mt) REVERT: B 5 LYS cc_start: 0.5251 (OUTLIER) cc_final: 0.5020 (tptp) REVERT: B 50 SER cc_start: 0.5380 (OUTLIER) cc_final: 0.4913 (m) REVERT: B 178 MET cc_start: 0.5839 (ttp) cc_final: 0.5632 (ttp) REVERT: B 212 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.5533 (t70) REVERT: B 379 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6969 (mmp) REVERT: B 439 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.5991 (mt) REVERT: B 457 SER cc_start: 0.7412 (OUTLIER) cc_final: 0.7060 (p) REVERT: B 491 LEU cc_start: 0.3635 (OUTLIER) cc_final: 0.2254 (tt) REVERT: B 659 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7699 (mt) outliers start: 143 outliers final: 45 residues processed: 294 average time/residue: 0.9718 time to fit residues: 314.0912 Evaluate side-chains 217 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 154 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN A 501 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN B 501 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11916 Z= 0.248 Angle : 0.825 15.093 16196 Z= 0.426 Chirality : 0.048 0.228 1818 Planarity : 0.007 0.076 2024 Dihedral : 11.982 66.031 1716 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 1.12 % Allowed : 10.15 % Favored : 88.73 % Rotamer: Outliers : 8.74 % Allowed : 29.05 % Favored : 62.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.56 (0.22), residues: 1428 helix: 0.56 (0.18), residues: 876 sheet: -3.20 (0.57), residues: 46 loop : -3.85 (0.23), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 75 HIS 0.003 0.001 HIS A 629 PHE 0.021 0.002 PHE B 33 TYR 0.021 0.001 TYR A 98 ARG 0.014 0.001 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 160 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 SER cc_start: 0.7342 (OUTLIER) cc_final: 0.6921 (p) REVERT: A 491 LEU cc_start: 0.2996 (OUTLIER) cc_final: 0.1751 (tt) REVERT: A 582 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7609 (mt) REVERT: A 691 MET cc_start: 0.5556 (mtm) cc_final: 0.5223 (mtp) REVERT: B 294 HIS cc_start: 0.4049 (OUTLIER) cc_final: 0.3361 (m-70) REVERT: B 457 SER cc_start: 0.7344 (OUTLIER) cc_final: 0.6910 (p) REVERT: B 491 LEU cc_start: 0.2848 (OUTLIER) cc_final: 0.1804 (tt) REVERT: B 582 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7610 (mt) REVERT: B 691 MET cc_start: 0.5557 (mtm) cc_final: 0.5223 (mtp) outliers start: 108 outliers final: 36 residues processed: 248 average time/residue: 1.0130 time to fit residues: 275.0238 Evaluate side-chains 192 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 149 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.0970 chunk 97 optimal weight: 0.0370 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN B 127 ASN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11916 Z= 0.218 Angle : 0.746 10.515 16196 Z= 0.383 Chirality : 0.045 0.201 1818 Planarity : 0.007 0.072 2024 Dihedral : 9.670 63.134 1650 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 1.05 % Allowed : 9.59 % Favored : 89.36 % Rotamer: Outliers : 7.69 % Allowed : 29.85 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1428 helix: 0.99 (0.18), residues: 876 sheet: -3.05 (0.57), residues: 46 loop : -3.60 (0.23), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 75 HIS 0.006 0.001 HIS A 294 PHE 0.025 0.001 PHE A 136 TYR 0.018 0.001 TYR B 98 ARG 0.006 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 144 time to evaluate : 1.321 Fit side-chains REVERT: A 76 MET cc_start: 0.6528 (mtt) cc_final: 0.6140 (mtt) REVERT: A 390 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.5871 (t80) REVERT: A 491 LEU cc_start: 0.2542 (OUTLIER) cc_final: 0.1280 (tt) REVERT: A 508 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.5174 (mmt) REVERT: A 642 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6308 (mp) REVERT: B 68 SER cc_start: 0.1532 (OUTLIER) cc_final: 0.1320 (p) REVERT: B 76 MET cc_start: 0.6514 (mtt) cc_final: 0.6111 (mtt) REVERT: B 294 HIS cc_start: 0.4019 (OUTLIER) cc_final: 0.3097 (m-70) REVERT: B 295 TYR cc_start: 0.4846 (OUTLIER) cc_final: 0.4307 (m-80) REVERT: B 491 LEU cc_start: 0.2434 (OUTLIER) cc_final: 0.1151 (tt) REVERT: B 508 MET cc_start: 0.5660 (OUTLIER) cc_final: 0.5079 (mtt) REVERT: B 642 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6302 (mp) outliers start: 95 outliers final: 28 residues processed: 224 average time/residue: 0.9652 time to fit residues: 238.2419 Evaluate side-chains 170 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 609 GLN A 710 GLN B 263 GLN B 270 ASN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN B 609 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11916 Z= 0.242 Angle : 0.756 10.223 16196 Z= 0.386 Chirality : 0.046 0.206 1818 Planarity : 0.006 0.072 2024 Dihedral : 8.652 59.593 1628 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.77 % Allowed : 9.66 % Favored : 89.57 % Rotamer: Outliers : 5.66 % Allowed : 31.88 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.77 (0.23), residues: 1428 helix: 1.13 (0.18), residues: 876 sheet: -3.08 (0.57), residues: 46 loop : -3.39 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 75 HIS 0.003 0.001 HIS A 629 PHE 0.022 0.002 PHE A 33 TYR 0.012 0.001 TYR B 98 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 136 time to evaluate : 1.383 Fit side-chains REVERT: A 390 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.5854 (t80) REVERT: A 491 LEU cc_start: 0.2246 (OUTLIER) cc_final: 0.0954 (tt) REVERT: A 642 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6178 (mp) REVERT: B 68 SER cc_start: 0.1151 (OUTLIER) cc_final: 0.0711 (p) REVERT: B 220 LEU cc_start: 0.7068 (mt) cc_final: 0.6822 (mt) REVERT: B 295 TYR cc_start: 0.4787 (OUTLIER) cc_final: 0.4320 (m-80) REVERT: B 390 PHE cc_start: 0.6515 (OUTLIER) cc_final: 0.5796 (t80) REVERT: B 491 LEU cc_start: 0.2161 (OUTLIER) cc_final: 0.0937 (tt) REVERT: B 642 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6175 (mp) outliers start: 70 outliers final: 34 residues processed: 198 average time/residue: 1.0491 time to fit residues: 227.9661 Evaluate side-chains 171 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 129 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11916 Z= 0.233 Angle : 0.725 9.777 16196 Z= 0.371 Chirality : 0.045 0.188 1818 Planarity : 0.006 0.070 2024 Dihedral : 8.117 59.272 1621 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.77 % Allowed : 9.10 % Favored : 90.13 % Rotamer: Outliers : 5.10 % Allowed : 33.09 % Favored : 61.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.23), residues: 1428 helix: 1.33 (0.18), residues: 874 sheet: -3.09 (0.57), residues: 46 loop : -3.18 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 625 HIS 0.004 0.001 HIS A 294 PHE 0.025 0.001 PHE B 33 TYR 0.013 0.001 TYR A 98 ARG 0.006 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 131 time to evaluate : 1.284 Fit side-chains REVERT: A 390 PHE cc_start: 0.6381 (OUTLIER) cc_final: 0.5753 (t80) REVERT: A 391 ILE cc_start: 0.5000 (OUTLIER) cc_final: 0.4372 (tt) REVERT: A 491 LEU cc_start: 0.2202 (OUTLIER) cc_final: 0.1043 (tt) REVERT: A 642 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6199 (mp) REVERT: B 68 SER cc_start: 0.0939 (OUTLIER) cc_final: 0.0300 (m) REVERT: B 220 LEU cc_start: 0.7055 (mt) cc_final: 0.6846 (mt) REVERT: B 295 TYR cc_start: 0.4690 (OUTLIER) cc_final: 0.4200 (m-80) REVERT: B 390 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.5739 (t80) REVERT: B 391 ILE cc_start: 0.5033 (OUTLIER) cc_final: 0.4407 (tt) REVERT: B 491 LEU cc_start: 0.2092 (OUTLIER) cc_final: 0.0905 (tt) REVERT: B 642 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6196 (mp) outliers start: 63 outliers final: 36 residues processed: 186 average time/residue: 0.9635 time to fit residues: 198.0919 Evaluate side-chains 176 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 130 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 77 optimal weight: 0.0370 chunk 115 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 31 GLN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11916 Z= 0.266 Angle : 0.745 10.722 16196 Z= 0.381 Chirality : 0.046 0.195 1818 Planarity : 0.006 0.072 2024 Dihedral : 7.726 57.486 1617 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.77 % Allowed : 9.59 % Favored : 89.64 % Rotamer: Outliers : 4.85 % Allowed : 33.09 % Favored : 62.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.23), residues: 1428 helix: 1.33 (0.18), residues: 876 sheet: -3.02 (0.59), residues: 46 loop : -3.13 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 625 HIS 0.009 0.001 HIS A 294 PHE 0.027 0.001 PHE B 33 TYR 0.012 0.001 TYR A 98 ARG 0.005 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 133 time to evaluate : 1.308 Fit side-chains REVERT: A 390 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.5858 (t80) REVERT: A 391 ILE cc_start: 0.5185 (OUTLIER) cc_final: 0.4541 (tt) REVERT: A 491 LEU cc_start: 0.2238 (OUTLIER) cc_final: 0.0953 (tt) REVERT: A 642 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6152 (mp) REVERT: B 220 LEU cc_start: 0.7024 (mt) cc_final: 0.6780 (mt) REVERT: B 295 TYR cc_start: 0.4848 (OUTLIER) cc_final: 0.4378 (m-80) REVERT: B 390 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.5843 (t80) REVERT: B 391 ILE cc_start: 0.5152 (OUTLIER) cc_final: 0.4516 (tt) REVERT: B 491 LEU cc_start: 0.2099 (OUTLIER) cc_final: 0.0793 (tt) REVERT: B 642 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6146 (mp) outliers start: 60 outliers final: 35 residues processed: 184 average time/residue: 0.9704 time to fit residues: 196.9310 Evaluate side-chains 179 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 135 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 26 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11916 Z= 0.216 Angle : 0.704 9.787 16196 Z= 0.359 Chirality : 0.045 0.325 1818 Planarity : 0.006 0.069 2024 Dihedral : 7.505 57.440 1617 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.38 % Favored : 89.99 % Rotamer: Outliers : 4.53 % Allowed : 33.01 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.24 (0.24), residues: 1428 helix: 1.49 (0.19), residues: 884 sheet: -2.92 (0.58), residues: 46 loop : -3.10 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 625 HIS 0.008 0.001 HIS A 294 PHE 0.028 0.001 PHE A 33 TYR 0.012 0.001 TYR B 98 ARG 0.006 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 133 time to evaluate : 1.355 Fit side-chains REVERT: A 390 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.5699 (t80) REVERT: A 491 LEU cc_start: 0.2076 (OUTLIER) cc_final: 0.0806 (tt) REVERT: A 642 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6273 (mp) REVERT: B 295 TYR cc_start: 0.4810 (OUTLIER) cc_final: 0.4213 (m-80) REVERT: B 301 LYS cc_start: 0.6151 (pptt) cc_final: 0.5822 (pptt) REVERT: B 390 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5689 (t80) REVERT: B 491 LEU cc_start: 0.2078 (OUTLIER) cc_final: 0.0849 (tt) REVERT: B 642 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6268 (mp) outliers start: 56 outliers final: 32 residues processed: 181 average time/residue: 1.0660 time to fit residues: 211.3470 Evaluate side-chains 169 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 11916 Z= 0.392 Angle : 0.803 9.826 16196 Z= 0.418 Chirality : 0.051 0.460 1818 Planarity : 0.007 0.078 2024 Dihedral : 7.589 58.702 1615 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.77 % Allowed : 9.94 % Favored : 89.29 % Rotamer: Outliers : 4.21 % Allowed : 33.01 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.62 (0.23), residues: 1428 helix: 1.13 (0.18), residues: 878 sheet: -2.83 (0.60), residues: 46 loop : -3.11 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 625 HIS 0.007 0.002 HIS A 294 PHE 0.028 0.002 PHE B 33 TYR 0.009 0.002 TYR A 614 ARG 0.004 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 1.179 Fit side-chains REVERT: A 390 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.6064 (t80) REVERT: A 491 LEU cc_start: 0.1972 (OUTLIER) cc_final: 0.0489 (tt) REVERT: A 544 LEU cc_start: 0.6916 (mt) cc_final: 0.6701 (mt) REVERT: A 642 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6199 (mp) REVERT: B 295 TYR cc_start: 0.5510 (OUTLIER) cc_final: 0.4833 (m-80) REVERT: B 390 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.5927 (t80) REVERT: B 394 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6284 (mp) REVERT: B 491 LEU cc_start: 0.1995 (OUTLIER) cc_final: 0.0603 (tt) REVERT: B 544 LEU cc_start: 0.6914 (mt) cc_final: 0.6699 (mt) REVERT: B 642 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6193 (mp) outliers start: 52 outliers final: 32 residues processed: 177 average time/residue: 1.0598 time to fit residues: 205.6390 Evaluate side-chains 170 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 chunk 141 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 ASN A 710 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN B 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11916 Z= 0.224 Angle : 0.714 9.639 16196 Z= 0.366 Chirality : 0.047 0.535 1818 Planarity : 0.006 0.071 2024 Dihedral : 7.301 58.134 1615 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.59 % Favored : 89.78 % Rotamer: Outliers : 3.64 % Allowed : 33.33 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.28 (0.23), residues: 1428 helix: 1.42 (0.18), residues: 888 sheet: -2.56 (0.76), residues: 34 loop : -3.11 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 625 HIS 0.006 0.001 HIS B 294 PHE 0.030 0.001 PHE A 33 TYR 0.012 0.001 TYR B 98 ARG 0.006 0.000 ARG B 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 129 time to evaluate : 1.100 Fit side-chains REVERT: A 390 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.5817 (t80) REVERT: A 391 ILE cc_start: 0.5055 (OUTLIER) cc_final: 0.4433 (tt) REVERT: A 491 LEU cc_start: 0.1815 (OUTLIER) cc_final: 0.0207 (tt) REVERT: A 642 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6291 (mp) REVERT: B 294 HIS cc_start: 0.3161 (OUTLIER) cc_final: 0.2354 (m-70) REVERT: B 295 TYR cc_start: 0.5082 (OUTLIER) cc_final: 0.4485 (m-80) REVERT: B 301 LYS cc_start: 0.6128 (pptt) cc_final: 0.5815 (pptt) REVERT: B 390 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.5658 (t80) REVERT: B 391 ILE cc_start: 0.4997 (OUTLIER) cc_final: 0.4381 (tt) REVERT: B 394 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6160 (mp) REVERT: B 491 LEU cc_start: 0.2053 (OUTLIER) cc_final: 0.0658 (tt) REVERT: B 642 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6255 (mp) outliers start: 45 outliers final: 28 residues processed: 170 average time/residue: 0.9955 time to fit residues: 185.7761 Evaluate side-chains 166 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.179820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128419 restraints weight = 13483.679| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.50 r_work: 0.3457 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11916 Z= 0.235 Angle : 0.715 9.565 16196 Z= 0.367 Chirality : 0.046 0.527 1818 Planarity : 0.006 0.072 2024 Dihedral : 7.097 59.895 1614 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.94 % Favored : 89.43 % Rotamer: Outliers : 3.32 % Allowed : 33.66 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.19 (0.23), residues: 1428 helix: 1.51 (0.18), residues: 890 sheet: -2.56 (0.75), residues: 34 loop : -3.16 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 625 HIS 0.007 0.001 HIS A 294 PHE 0.030 0.001 PHE A 33 TYR 0.011 0.001 TYR A 98 ARG 0.005 0.000 ARG B 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5258.16 seconds wall clock time: 92 minutes 51.73 seconds (5571.73 seconds total)