Starting phenix.real_space_refine on Sat Apr 6 08:54:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/04_2024/8d43_27173.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/04_2024/8d43_27173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/04_2024/8d43_27173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/04_2024/8d43_27173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/04_2024/8d43_27173.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/04_2024/8d43_27173.pdb" } resolution = 2.88 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= -0.000 sd= 0.045 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 Ca 2 9.91 5 S 35 5.16 5 C 4926 2.51 5 N 1346 2.21 5 O 1454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 42": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A GLU 656": "OE1" <-> "OE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7763 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6952 Classifications: {'peptide': 862} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 801} Chain breaks: 2 Chain: "B" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 758 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.88, per 1000 atoms: 0.63 Number of scatterers: 7763 At special positions: 0 Unit cell: (70.62, 88.81, 116.63, 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) Ca 2 19.99 S 35 16.00 O 1454 8.00 N 1346 7.00 C 4926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 99 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN A 97 " Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.5 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 22.3% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.624A pdb=" N VAL A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 453 through 459 removed outlier: 3.799A pdb=" N LYS A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.517A pdb=" N GLY A 565 " --> pdb=" O HIS A 562 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 566 " --> pdb=" O TYR A 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 566' Processing helix chain 'A' and resid 571 through 592 removed outlier: 4.340A pdb=" N GLY A 576 " --> pdb=" O HIS A 572 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.689A pdb=" N ARG A 610 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 611 " --> pdb=" O SER A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 611' Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 628 through 639 removed outlier: 3.875A pdb=" N VAL A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 668 Processing helix chain 'A' and resid 685 through 689 removed outlier: 3.912A pdb=" N LEU A 689 " --> pdb=" O PRO A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.597A pdb=" N ILE A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 697 " --> pdb=" O HIS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 721 Processing helix chain 'A' and resid 728 through 733 removed outlier: 4.203A pdb=" N GLN A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 removed outlier: 4.113A pdb=" N ASN A 741 " --> pdb=" O THR A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 Processing helix chain 'A' and resid 852 through 857 removed outlier: 3.812A pdb=" N THR A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.390A pdb=" N HIS B 29 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 removed outlier: 3.830A pdb=" N MET A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS A 255 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 133 removed outlier: 5.579A pdb=" N VAL A 130 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A 141 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR A 147 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 167 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 133 removed outlier: 5.579A pdb=" N VAL A 130 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A 141 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR A 147 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 167 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 321 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA6, first strand: chain 'A' and resid 644 through 645 removed outlier: 6.870A pdb=" N VAL A 614 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 599 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TRP A 615 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 601 " --> pdb=" O TRP A 615 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 600 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 463 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N TRP A 540 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA A 465 " --> pdb=" O TRP A 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AA8, first strand: chain 'A' and resid 726 through 727 removed outlier: 3.941A pdb=" N LEU A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 764 through 769 Processing sheet with id=AB1, first strand: chain 'A' and resid 808 through 812 removed outlier: 6.129A pdb=" N ILE A 828 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 891 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP A 888 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY A 932 " --> pdb=" O TRP A 888 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU A 890 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 916 " --> pdb=" O ARG A 929 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 840 through 846 removed outlier: 3.596A pdb=" N TRP A 939 " --> pdb=" O SER A 874 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AB4, first strand: chain 'B' and resid 74 through 77 273 hydrogen bonds defined for protein. 714 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: 2.96 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2400 1.33 - 1.46: 1518 1.46 - 1.58: 4014 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 7985 Sorted by residual: bond pdb=" CA SER A 506 " pdb=" C SER A 506 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.22e-02 6.72e+03 7.99e+00 bond pdb=" CA ASP B 101 " pdb=" C ASP B 101 " ideal model delta sigma weight residual 1.525 1.493 0.031 1.28e-02 6.10e+03 5.99e+00 bond pdb=" C CYS B 70 " pdb=" O CYS B 70 " ideal model delta sigma weight residual 1.240 1.214 0.025 1.16e-02 7.43e+03 4.68e+00 bond pdb=" CA ILE B 46 " pdb=" C ILE B 46 " ideal model delta sigma weight residual 1.522 1.506 0.016 8.30e-03 1.45e+04 3.58e+00 bond pdb=" C ARG A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.32e-02 5.74e+03 3.57e+00 ... (remaining 7980 not shown) Histogram of bond angle deviations from ideal: 97.58 - 104.95: 209 104.95 - 112.32: 3872 112.32 - 119.69: 2823 119.69 - 127.05: 3824 127.05 - 134.42: 145 Bond angle restraints: 10873 Sorted by residual: angle pdb=" N SER A 506 " pdb=" CA SER A 506 " pdb=" C SER A 506 " ideal model delta sigma weight residual 108.96 98.00 10.96 1.59e+00 3.96e-01 4.75e+01 angle pdb=" C ARG A 110 " pdb=" N PRO A 111 " pdb=" CA PRO A 111 " ideal model delta sigma weight residual 119.76 113.52 6.24 1.00e+00 1.00e+00 3.89e+01 angle pdb=" N ASP B 101 " pdb=" CA ASP B 101 " pdb=" C ASP B 101 " ideal model delta sigma weight residual 108.20 97.58 10.62 1.71e+00 3.42e-01 3.86e+01 angle pdb=" N GLY B 61 " pdb=" CA GLY B 61 " pdb=" C GLY B 61 " ideal model delta sigma weight residual 115.64 108.38 7.26 1.46e+00 4.69e-01 2.48e+01 angle pdb=" N TRP A 503 " pdb=" CA TRP A 503 " pdb=" CB TRP A 503 " ideal model delta sigma weight residual 110.39 117.49 -7.10 1.61e+00 3.86e-01 1.94e+01 ... (remaining 10868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.49: 4254 24.49 - 48.98: 423 48.98 - 73.47: 62 73.47 - 97.95: 22 97.95 - 122.44: 8 Dihedral angle restraints: 4769 sinusoidal: 1995 harmonic: 2774 Sorted by residual: dihedral pdb=" N TRP A 503 " pdb=" C TRP A 503 " pdb=" CA TRP A 503 " pdb=" CB TRP A 503 " ideal model delta harmonic sigma weight residual 122.80 136.80 -14.00 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" C TRP A 503 " pdb=" N TRP A 503 " pdb=" CA TRP A 503 " pdb=" CB TRP A 503 " ideal model delta harmonic sigma weight residual -122.60 -133.76 11.16 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" O2 MAN C 4 " pdb=" C2 MAN C 4 " pdb=" C3 MAN C 4 " pdb=" O3 MAN C 4 " ideal model delta sinusoidal sigma weight residual -57.63 64.81 -122.44 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 4766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1067 0.102 - 0.205: 80 0.205 - 0.307: 6 0.307 - 0.410: 1 0.410 - 0.512: 1 Chirality restraints: 1155 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.32e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.22e+01 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.33 0.07 2.00e-02 2.50e+03 1.14e+01 ... (remaining 1152 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.143 2.00e-02 2.50e+03 1.19e-01 1.76e+02 pdb=" C7 NAG C 1 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.191 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 503 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO A 504 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 826 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO A 827 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 827 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 827 " 0.032 5.00e-02 4.00e+02 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 1 2.08 - 2.78: 1750 2.78 - 3.49: 10223 3.49 - 4.19: 20876 4.19 - 4.90: 35979 Nonbonded interactions: 68829 Sorted by model distance: nonbonded pdb=" OD2 ASP B 57 " pdb="CA CA B 602 " model vdw 1.371 2.510 nonbonded pdb=" OE2 GLU B 105 " pdb="CA CA B 601 " model vdw 2.091 2.510 nonbonded pdb=" OD1 ASP B 94 " pdb="CA CA B 601 " model vdw 2.112 2.510 nonbonded pdb=" OD1 ASP B 53 " pdb="CA CA B 602 " model vdw 2.177 2.510 nonbonded pdb=" O VAL B 96 " pdb="CA CA B 601 " model vdw 2.194 2.510 ... (remaining 68824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 9.270 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.440 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0171 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7985 Z= 0.280 Angle : 0.842 10.960 10873 Z= 0.482 Chirality : 0.057 0.512 1155 Planarity : 0.007 0.119 1426 Dihedral : 19.690 122.443 2981 Min Nonbonded Distance : 1.371 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.48 % Allowed : 26.82 % Favored : 67.70 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.26), residues: 954 helix: -1.16 (0.40), residues: 160 sheet: -0.25 (0.33), residues: 223 loop : -1.24 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 503 HIS 0.008 0.001 HIS A 432 PHE 0.016 0.002 PHE A 101 TYR 0.011 0.001 TYR A 287 ARG 0.009 0.001 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 65 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.2636 (ttp80) cc_final: 0.2126 (tpm170) REVERT: A 310 ASP cc_start: 0.0472 (OUTLIER) cc_final: 0.0269 (m-30) REVERT: A 446 PHE cc_start: -0.0472 (m-80) cc_final: -0.1924 (m-80) REVERT: A 635 SER cc_start: -0.0488 (OUTLIER) cc_final: -0.0979 (t) REVERT: A 708 LEU cc_start: -0.1898 (OUTLIER) cc_final: -0.2332 (mp) REVERT: A 781 SER cc_start: -0.2229 (OUTLIER) cc_final: -0.3649 (t) REVERT: A 814 MET cc_start: 0.1756 (mmt) cc_final: -0.0771 (tpp) outliers start: 46 outliers final: 13 residues processed: 110 average time/residue: 0.8830 time to fit residues: 105.3997 Evaluate side-chains 53 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 36 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 HIS A 732 GLN A 785 HIS A 919 HIS A 934 ASN A 942 HIS B 27 ASN B 28 HIS B 29 HIS B 93 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0672 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7985 Z= 0.292 Angle : 0.801 13.990 10873 Z= 0.396 Chirality : 0.050 0.196 1155 Planarity : 0.007 0.072 1426 Dihedral : 10.158 78.903 1170 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 7.87 % Allowed : 23.00 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.27), residues: 954 helix: -0.80 (0.36), residues: 162 sheet: -0.41 (0.33), residues: 224 loop : -1.09 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 520 HIS 0.011 0.002 HIS A 678 PHE 0.023 0.003 PHE A 651 TYR 0.023 0.003 TYR A 509 ARG 0.008 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 42 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: -0.1232 (OUTLIER) cc_final: -0.1564 (tp) REVERT: A 259 ILE cc_start: 0.2190 (pt) cc_final: 0.0893 (mt) REVERT: A 628 ILE cc_start: 0.2026 (OUTLIER) cc_final: 0.1572 (pp) REVERT: A 635 SER cc_start: 0.0554 (OUTLIER) cc_final: -0.0248 (t) REVERT: A 656 GLU cc_start: 0.0021 (OUTLIER) cc_final: -0.2544 (mm-30) REVERT: A 707 LEU cc_start: 0.0509 (OUTLIER) cc_final: 0.0156 (mp) REVERT: A 743 ASP cc_start: -0.1201 (OUTLIER) cc_final: -0.1745 (p0) REVERT: A 744 ASP cc_start: 0.0391 (OUTLIER) cc_final: 0.0048 (p0) REVERT: A 745 GLN cc_start: -0.1144 (OUTLIER) cc_final: -0.1653 (mp10) REVERT: A 814 MET cc_start: 0.1814 (mmt) cc_final: -0.1977 (tpp) outliers start: 66 outliers final: 20 residues processed: 99 average time/residue: 0.9229 time to fit residues: 99.2466 Evaluate side-chains 64 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 36 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 812 ARG Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 670 GLN A 732 GLN A 804 GLN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1275 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 7985 Z= 0.303 Angle : 0.803 12.258 10873 Z= 0.395 Chirality : 0.049 0.165 1155 Planarity : 0.007 0.055 1426 Dihedral : 8.016 83.480 1153 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.65 % Favored : 92.24 % Rotamer: Outliers : 7.27 % Allowed : 24.08 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.26), residues: 954 helix: -1.16 (0.33), residues: 163 sheet: -0.25 (0.34), residues: 228 loop : -1.19 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP A 355 HIS 0.008 0.002 HIS A 255 PHE 0.027 0.003 PHE A 845 TYR 0.020 0.003 TYR A 669 ARG 0.009 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 50 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.1951 (pt) cc_final: 0.1734 (pt) REVERT: A 259 ILE cc_start: 0.2427 (OUTLIER) cc_final: 0.1987 (pp) REVERT: A 351 THR cc_start: 0.4787 (OUTLIER) cc_final: 0.4326 (t) REVERT: A 609 GLN cc_start: 0.2521 (OUTLIER) cc_final: 0.1984 (pm20) REVERT: A 635 SER cc_start: 0.1475 (OUTLIER) cc_final: 0.0617 (m) REVERT: A 656 GLU cc_start: 0.0461 (OUTLIER) cc_final: -0.1336 (tm-30) REVERT: A 712 TYR cc_start: 0.0246 (OUTLIER) cc_final: -0.0303 (t80) REVERT: A 813 TRP cc_start: 0.0574 (OUTLIER) cc_final: -0.0435 (m-10) outliers start: 61 outliers final: 18 residues processed: 103 average time/residue: 0.8877 time to fit residues: 99.6330 Evaluate side-chains 66 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 41 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 86 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 77 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 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS A 171 ASN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1628 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7985 Z= 0.265 Angle : 0.777 17.671 10873 Z= 0.378 Chirality : 0.048 0.175 1155 Planarity : 0.007 0.060 1426 Dihedral : 7.493 89.227 1150 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.76 % Favored : 92.14 % Rotamer: Outliers : 4.65 % Allowed : 27.53 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.26), residues: 954 helix: -1.26 (0.34), residues: 171 sheet: -0.31 (0.34), residues: 229 loop : -1.51 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 355 HIS 0.009 0.002 HIS A 77 PHE 0.021 0.002 PHE A 845 TYR 0.030 0.003 TYR A 477 ARG 0.024 0.001 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 51 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.1734 (OUTLIER) cc_final: 0.1502 (tt) REVERT: A 142 MET cc_start: 0.2476 (mpp) cc_final: 0.0097 (tpp) REVERT: A 259 ILE cc_start: 0.2762 (OUTLIER) cc_final: 0.2261 (pp) REVERT: A 281 ASN cc_start: 0.1977 (OUTLIER) cc_final: 0.1665 (m-40) REVERT: A 309 ARG cc_start: 0.2333 (OUTLIER) cc_final: 0.0997 (ptp90) REVERT: A 347 GLU cc_start: 0.4723 (mm-30) cc_final: 0.3952 (pt0) REVERT: A 483 LEU cc_start: 0.3725 (OUTLIER) cc_final: 0.2843 (tp) REVERT: A 615 TRP cc_start: 0.0084 (OUTLIER) cc_final: -0.0339 (p90) REVERT: A 712 TYR cc_start: 0.0716 (OUTLIER) cc_final: -0.0035 (t80) outliers start: 39 outliers final: 16 residues processed: 81 average time/residue: 0.8784 time to fit residues: 77.8365 Evaluate side-chains 67 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 44 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 91 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 0.2980 chunk 64 optimal weight: 0.1980 chunk 0 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1776 moved from start: 0.7201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7985 Z= 0.229 Angle : 0.715 12.794 10873 Z= 0.343 Chirality : 0.046 0.155 1155 Planarity : 0.006 0.058 1426 Dihedral : 6.924 84.517 1148 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.55 % Favored : 92.35 % Rotamer: Outliers : 4.05 % Allowed : 28.01 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.26), residues: 954 helix: -0.84 (0.35), residues: 168 sheet: -0.29 (0.35), residues: 228 loop : -1.58 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 730 HIS 0.004 0.001 HIS A 572 PHE 0.017 0.002 PHE A 611 TYR 0.017 0.002 TYR A 746 ARG 0.008 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 48 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.2602 (mpp) cc_final: 0.0234 (tpp) REVERT: A 259 ILE cc_start: 0.2823 (OUTLIER) cc_final: 0.2419 (pp) REVERT: A 310 ASP cc_start: 0.1818 (OUTLIER) cc_final: 0.1397 (m-30) REVERT: A 347 GLU cc_start: 0.4972 (mm-30) cc_final: 0.4454 (pt0) REVERT: A 543 MET cc_start: 0.1591 (mtt) cc_final: 0.0525 (tpp) REVERT: A 594 MET cc_start: 0.1633 (mmm) cc_final: 0.1280 (ppp) REVERT: A 712 TYR cc_start: 0.0640 (OUTLIER) cc_final: -0.0064 (t80) REVERT: A 726 MET cc_start: 0.2794 (mtp) cc_final: 0.2569 (ptm) outliers start: 34 outliers final: 18 residues processed: 80 average time/residue: 0.8065 time to fit residues: 71.0429 Evaluate side-chains 62 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 41 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.0470 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS A 676 HIS A 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2039 moved from start: 0.8243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7985 Z= 0.226 Angle : 0.717 11.653 10873 Z= 0.351 Chirality : 0.045 0.147 1155 Planarity : 0.006 0.068 1426 Dihedral : 6.480 76.170 1148 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.55 % Favored : 92.35 % Rotamer: Outliers : 3.81 % Allowed : 28.13 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.26), residues: 954 helix: -0.79 (0.35), residues: 172 sheet: -0.22 (0.35), residues: 224 loop : -1.69 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 687 HIS 0.013 0.001 HIS A 568 PHE 0.014 0.002 PHE A 101 TYR 0.025 0.002 TYR A 60 ARG 0.011 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 48 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.4209 (t) cc_final: 0.3752 (t) REVERT: A 142 MET cc_start: 0.3027 (OUTLIER) cc_final: 0.0576 (tpp) REVERT: A 259 ILE cc_start: 0.3159 (OUTLIER) cc_final: 0.2694 (pp) REVERT: A 309 ARG cc_start: 0.3198 (OUTLIER) cc_final: 0.1495 (ptp90) REVERT: A 310 ASP cc_start: 0.2015 (OUTLIER) cc_final: 0.1212 (p0) REVERT: A 594 MET cc_start: 0.1674 (mmm) cc_final: 0.1391 (ppp) REVERT: A 615 TRP cc_start: -0.0576 (OUTLIER) cc_final: -0.0928 (p90) REVERT: A 712 TYR cc_start: 0.0693 (OUTLIER) cc_final: 0.0056 (t80) REVERT: A 715 LEU cc_start: -0.2294 (OUTLIER) cc_final: -0.2502 (mm) REVERT: A 813 TRP cc_start: 0.0969 (OUTLIER) cc_final: 0.0075 (m-10) outliers start: 32 outliers final: 13 residues processed: 72 average time/residue: 0.8675 time to fit residues: 68.8056 Evaluate side-chains 63 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 42 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain B residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 HIS A 181 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN A 676 HIS A 719 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2526 moved from start: 0.9790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7985 Z= 0.285 Angle : 0.771 11.108 10873 Z= 0.385 Chirality : 0.048 0.179 1155 Planarity : 0.007 0.070 1426 Dihedral : 6.324 62.261 1147 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.07 % Favored : 91.82 % Rotamer: Outliers : 4.77 % Allowed : 27.65 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.26), residues: 954 helix: -0.89 (0.36), residues: 164 sheet: -0.23 (0.37), residues: 214 loop : -1.58 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP A 730 HIS 0.012 0.002 HIS A 568 PHE 0.021 0.002 PHE A 525 TYR 0.020 0.002 TYR A 746 ARG 0.014 0.001 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 53 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.6033 (mm-30) cc_final: 0.5722 (tt0) REVERT: A 142 MET cc_start: 0.3454 (OUTLIER) cc_final: 0.1104 (tpt) REVERT: A 242 MET cc_start: 0.0838 (OUTLIER) cc_final: 0.0507 (pmm) REVERT: A 259 ILE cc_start: 0.3613 (OUTLIER) cc_final: 0.3032 (pp) REVERT: A 281 ASN cc_start: 0.2331 (OUTLIER) cc_final: 0.2063 (m-40) REVERT: A 524 MET cc_start: 0.1455 (tmm) cc_final: 0.0100 (ptm) REVERT: A 594 MET cc_start: 0.2159 (mmm) cc_final: 0.1789 (ppp) REVERT: A 615 TRP cc_start: -0.0242 (OUTLIER) cc_final: -0.0836 (p90) REVERT: A 670 GLN cc_start: 0.1239 (OUTLIER) cc_final: 0.0181 (pt0) REVERT: A 697 ILE cc_start: 0.1744 (OUTLIER) cc_final: 0.1381 (mt) REVERT: A 712 TYR cc_start: 0.0744 (OUTLIER) cc_final: 0.0149 (t80) REVERT: A 715 LEU cc_start: -0.1954 (OUTLIER) cc_final: -0.2227 (mm) REVERT: A 744 ASP cc_start: 0.3394 (OUTLIER) cc_final: 0.3174 (p0) REVERT: A 813 TRP cc_start: 0.1112 (OUTLIER) cc_final: 0.0227 (m-10) outliers start: 40 outliers final: 15 residues processed: 85 average time/residue: 0.8569 time to fit residues: 80.0060 Evaluate side-chains 67 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 41 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 0.0000 chunk 63 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 GLN ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2596 moved from start: 1.0267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 7985 Z= 0.233 Angle : 0.731 17.629 10873 Z= 0.349 Chirality : 0.044 0.162 1155 Planarity : 0.005 0.059 1426 Dihedral : 5.827 56.480 1146 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.18 % Favored : 93.71 % Rotamer: Outliers : 3.81 % Allowed : 29.32 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.26), residues: 954 helix: -0.39 (0.38), residues: 162 sheet: -0.01 (0.36), residues: 214 loop : -1.62 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 687 HIS 0.009 0.001 HIS A 568 PHE 0.048 0.002 PHE A 101 TYR 0.019 0.002 TYR B 86 ARG 0.005 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 49 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.6054 (mm-30) cc_final: 0.5771 (tt0) REVERT: A 96 LYS cc_start: 0.5082 (mttm) cc_final: 0.4750 (tptp) REVERT: A 226 TRP cc_start: 0.4122 (m-90) cc_final: 0.3868 (m-90) REVERT: A 242 MET cc_start: 0.1844 (OUTLIER) cc_final: 0.0852 (pmm) REVERT: A 259 ILE cc_start: 0.3857 (OUTLIER) cc_final: 0.3358 (pp) REVERT: A 310 ASP cc_start: 0.3393 (OUTLIER) cc_final: 0.3034 (m-30) REVERT: A 405 ASP cc_start: 0.1593 (p0) cc_final: 0.1370 (p0) REVERT: A 524 MET cc_start: 0.1414 (tmm) cc_final: 0.0199 (ptm) REVERT: A 594 MET cc_start: 0.1944 (mmm) cc_final: 0.1634 (ppp) REVERT: A 715 LEU cc_start: -0.2004 (OUTLIER) cc_final: -0.2263 (mm) REVERT: A 813 TRP cc_start: 0.0926 (OUTLIER) cc_final: 0.0322 (m-10) outliers start: 32 outliers final: 10 residues processed: 73 average time/residue: 1.0052 time to fit residues: 80.3121 Evaluate side-chains 56 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain B residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.0670 chunk 88 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 0.0070 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2824 moved from start: 1.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7985 Z= 0.228 Angle : 0.723 11.108 10873 Z= 0.356 Chirality : 0.045 0.172 1155 Planarity : 0.006 0.059 1426 Dihedral : 5.697 55.236 1146 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 2.98 % Allowed : 30.15 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.26), residues: 954 helix: -0.38 (0.38), residues: 163 sheet: -0.12 (0.35), residues: 219 loop : -1.63 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 322 HIS 0.014 0.001 HIS A 305 PHE 0.039 0.002 PHE A 101 TYR 0.018 0.002 TYR B 86 ARG 0.007 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 49 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.4773 (mttm) cc_final: 0.4484 (tptp) REVERT: A 310 ASP cc_start: 0.3128 (OUTLIER) cc_final: 0.2836 (m-30) REVERT: A 524 MET cc_start: 0.1651 (tmm) cc_final: 0.0305 (ptm) REVERT: A 543 MET cc_start: 0.2036 (mtt) cc_final: 0.1655 (mtm) REVERT: A 615 TRP cc_start: -0.0881 (OUTLIER) cc_final: -0.1437 (p90) REVERT: A 662 ARG cc_start: 0.2769 (OUTLIER) cc_final: 0.2237 (mtt-85) REVERT: A 712 TYR cc_start: 0.1010 (OUTLIER) cc_final: 0.0409 (t80) REVERT: A 715 LEU cc_start: -0.1793 (OUTLIER) cc_final: -0.2099 (mm) REVERT: A 744 ASP cc_start: 0.3883 (OUTLIER) cc_final: 0.3468 (p0) REVERT: A 813 TRP cc_start: 0.1036 (OUTLIER) cc_final: 0.0417 (m-10) outliers start: 25 outliers final: 11 residues processed: 70 average time/residue: 0.8768 time to fit residues: 67.2558 Evaluate side-chains 66 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ARG Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain B residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.0970 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 88 optimal weight: 0.1980 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 0.0060 chunk 58 optimal weight: 0.2980 chunk 46 optimal weight: 0.0670 chunk 60 optimal weight: 0.0770 chunk 81 optimal weight: 0.8980 overall best weight: 0.0890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2723 moved from start: 1.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7985 Z= 0.180 Angle : 0.677 11.705 10873 Z= 0.328 Chirality : 0.044 0.157 1155 Planarity : 0.005 0.057 1426 Dihedral : 5.352 55.869 1146 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.44 % Rotamer: Outliers : 1.79 % Allowed : 31.23 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.27), residues: 954 helix: -0.20 (0.38), residues: 170 sheet: 0.03 (0.35), residues: 222 loop : -1.43 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 322 HIS 0.006 0.001 HIS A 568 PHE 0.040 0.002 PHE A 101 TYR 0.012 0.001 TYR B 86 ARG 0.006 0.000 ARG A 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 TYR cc_start: 0.7292 (m-80) cc_final: 0.6872 (m-80) REVERT: A 98 MET cc_start: 0.2778 (mmm) cc_final: 0.2408 (mmm) REVERT: A 259 ILE cc_start: 0.3824 (mt) cc_final: 0.3012 (pp) REVERT: A 269 LYS cc_start: 0.6921 (tppt) cc_final: 0.6265 (ttmt) REVERT: A 310 ASP cc_start: 0.3108 (OUTLIER) cc_final: 0.2857 (m-30) REVERT: A 524 MET cc_start: 0.1338 (tmm) cc_final: 0.0370 (ptm) REVERT: A 615 TRP cc_start: -0.1377 (OUTLIER) cc_final: -0.1671 (p90) REVERT: A 629 SER cc_start: 0.3518 (OUTLIER) cc_final: 0.3315 (p) REVERT: A 712 TYR cc_start: 0.0800 (OUTLIER) cc_final: 0.0293 (t80) REVERT: A 715 LEU cc_start: -0.2052 (OUTLIER) cc_final: -0.2330 (mm) REVERT: A 813 TRP cc_start: 0.0726 (OUTLIER) cc_final: -0.0094 (m-90) REVERT: A 823 MET cc_start: 0.4339 (tmt) cc_final: 0.4112 (tmt) outliers start: 15 outliers final: 8 residues processed: 64 average time/residue: 0.7736 time to fit residues: 54.7124 Evaluate side-chains 60 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain B residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.280011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.265696 restraints weight = 9577.418| |-----------------------------------------------------------------------------| r_work (start): 0.4763 rms_B_bonded: 1.55 r_work: 0.4712 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.4626 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3635 moved from start: 1.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 7985 Z= 0.305 Angle : 0.862 11.463 10873 Z= 0.432 Chirality : 0.051 0.225 1155 Planarity : 0.007 0.060 1426 Dihedral : 6.009 51.904 1146 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.91 % Favored : 90.88 % Rotamer: Outliers : 3.34 % Allowed : 29.80 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.26), residues: 954 helix: -0.88 (0.36), residues: 168 sheet: -0.19 (0.35), residues: 211 loop : -1.72 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 322 HIS 0.016 0.002 HIS A 568 PHE 0.039 0.003 PHE A 101 TYR 0.027 0.003 TYR A 669 ARG 0.008 0.001 ARG A 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2798.85 seconds wall clock time: 51 minutes 19.83 seconds (3079.83 seconds total)