Starting phenix.real_space_refine on Thu Jan 18 04:29:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/01_2024/8d43_27173.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/01_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_27173/01_2024/8d43_27173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/01_2024/8d43_27173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/01_2024/8d43_27173.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/01_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 9 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: 5.00, per 1000 atoms: 0.64 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: 4.05 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: 1.05 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: 3.44 Time building geometry restraints manager: 3.86 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 - 21.46: 4126 21.46 - 42.91: 494 42.91 - 64.37: 106 64.37 - 85.82: 18 85.82 - 107.28: 6 Dihedral angle restraints: 4750 sinusoidal: 1976 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=" CA ASN A 97 " pdb=" C ASN A 97 " pdb=" N MET A 98 " pdb=" CA MET A 98 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 4747 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: 3.270 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: 9.720 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.720 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.760 ------------------------------------------------------------------------------- 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 : 18.875 107.278 2962 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 : 0.853 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: 0.8952 time to fit residues: 107.0180 Evaluate side-chains 53 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 36 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.0611 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7985 Z= 0.280 Angle : 0.765 12.918 10873 Z= 0.382 Chirality : 0.048 0.180 1155 Planarity : 0.007 0.068 1426 Dihedral : 9.306 78.756 1151 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 7.27 % Allowed : 23.48 % Favored : 69.25 % 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: -1.28 (0.27), residues: 954 helix: -0.66 (0.36), residues: 162 sheet: -0.39 (0.33), residues: 224 loop : -1.08 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 520 HIS 0.009 0.002 HIS A 255 PHE 0.026 0.003 PHE A 651 TYR 0.022 0.002 TYR A 509 ARG 0.009 0.001 ARG A 354 *********************** 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 102 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 41 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: -0.1293 (OUTLIER) cc_final: -0.1640 (tp) REVERT: A 259 ILE cc_start: 0.2102 (pt) cc_final: 0.0797 (mt) REVERT: A 628 ILE cc_start: 0.2164 (OUTLIER) cc_final: 0.1731 (pp) REVERT: A 635 SER cc_start: 0.0415 (OUTLIER) cc_final: -0.0463 (m) REVERT: A 656 GLU cc_start: -0.0104 (OUTLIER) cc_final: -0.1040 (mt-10) REVERT: A 743 ASP cc_start: -0.1250 (OUTLIER) cc_final: -0.1695 (p0) REVERT: A 744 ASP cc_start: 0.0203 (OUTLIER) cc_final: -0.0030 (p0) REVERT: A 745 GLN cc_start: -0.1442 (OUTLIER) cc_final: -0.1817 (mp10) REVERT: A 814 MET cc_start: 0.1700 (mmt) cc_final: -0.1927 (tpp) outliers start: 61 outliers final: 19 residues processed: 94 average time/residue: 0.9253 time to fit residues: 94.5601 Evaluate side-chains 58 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 32 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 581 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 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 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: 4.9990 chunk 72 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 86 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 HIS ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0704 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7985 Z= 0.199 Angle : 0.624 8.933 10873 Z= 0.306 Chirality : 0.045 0.214 1155 Planarity : 0.005 0.053 1426 Dihedral : 7.529 82.030 1134 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.65 % Allowed : 26.46 % Favored : 68.89 % 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: -1.03 (0.27), residues: 954 helix: -0.17 (0.38), residues: 162 sheet: -0.35 (0.33), residues: 235 loop : -0.96 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 687 HIS 0.006 0.001 HIS B 29 PHE 0.013 0.002 PHE A 538 TYR 0.013 0.001 TYR A 669 ARG 0.003 0.001 ARG A 704 *********************** 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 81 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 42 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLU cc_start: -0.1182 (OUTLIER) cc_final: -0.2584 (tp30) REVERT: A 242 MET cc_start: -0.1866 (ttp) cc_final: -0.2299 (ptp) REVERT: A 259 ILE cc_start: 0.1959 (OUTLIER) cc_final: 0.1088 (mt) REVERT: A 310 ASP cc_start: 0.0825 (OUTLIER) cc_final: 0.0312 (m-30) REVERT: A 594 MET cc_start: 0.0842 (mmm) cc_final: 0.0425 (pmm) REVERT: A 628 ILE cc_start: 0.1931 (OUTLIER) cc_final: 0.1283 (pp) REVERT: A 635 SER cc_start: 0.0424 (OUTLIER) cc_final: -0.0294 (m) REVERT: A 656 GLU cc_start: 0.0152 (OUTLIER) cc_final: -0.1562 (tm-30) REVERT: A 745 GLN cc_start: -0.0819 (OUTLIER) cc_final: -0.1457 (mp10) REVERT: A 812 ARG cc_start: 0.3521 (OUTLIER) cc_final: 0.2344 (mtt-85) REVERT: A 814 MET cc_start: 0.1989 (mmt) cc_final: -0.1852 (tpp) outliers start: 39 outliers final: 18 residues processed: 77 average time/residue: 1.0009 time to fit residues: 83.3044 Evaluate side-chains 59 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 33 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 554 VAL 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 699 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 823 MET Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 0.0980 chunk 92 optimal weight: 0.0000 chunk 83 optimal weight: 0.0770 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 0.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0851 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7985 Z= 0.193 Angle : 0.630 11.478 10873 Z= 0.303 Chirality : 0.044 0.137 1155 Planarity : 0.005 0.054 1426 Dihedral : 6.876 82.798 1133 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.29 % Allowed : 27.65 % 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: -1.00 (0.27), residues: 954 helix: -0.13 (0.37), residues: 163 sheet: -0.24 (0.34), residues: 228 loop : -0.99 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 730 HIS 0.010 0.001 HIS A 77 PHE 0.010 0.001 PHE A 538 TYR 0.015 0.002 TYR B 86 ARG 0.008 0.001 ARG A 173 *********************** 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 70 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 34 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 ILE cc_start: 0.2106 (OUTLIER) cc_final: 0.1521 (mp) REVERT: A 594 MET cc_start: 0.0966 (mmm) cc_final: 0.0449 (pmm) REVERT: A 628 ILE cc_start: 0.1652 (OUTLIER) cc_final: 0.0832 (pp) REVERT: A 635 SER cc_start: 0.0590 (OUTLIER) cc_final: -0.0224 (m) REVERT: A 656 GLU cc_start: 0.0436 (OUTLIER) cc_final: -0.1278 (tm-30) REVERT: A 698 ARG cc_start: 0.1923 (OUTLIER) cc_final: 0.1228 (mmm160) REVERT: A 712 TYR cc_start: 0.0196 (OUTLIER) cc_final: -0.0264 (t80) REVERT: A 745 GLN cc_start: -0.0798 (OUTLIER) cc_final: -0.1629 (mt0) REVERT: A 814 MET cc_start: 0.1813 (mmt) cc_final: -0.2251 (tpp) outliers start: 36 outliers final: 20 residues processed: 66 average time/residue: 1.0026 time to fit residues: 72.4116 Evaluate side-chains 56 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 29 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 554 VAL 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 687 TRP Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 712 TYR 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 823 MET Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1626 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7985 Z= 0.285 Angle : 0.825 17.152 10873 Z= 0.404 Chirality : 0.049 0.177 1155 Planarity : 0.007 0.090 1426 Dihedral : 7.118 84.058 1133 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 6.20 % Allowed : 26.58 % Favored : 67.22 % 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: -1.62 (0.26), residues: 954 helix: -1.00 (0.34), residues: 168 sheet: -0.24 (0.34), residues: 228 loop : -1.48 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 355 HIS 0.015 0.002 HIS A 572 PHE 0.028 0.003 PHE A 845 TYR 0.043 0.003 TYR A 489 ARG 0.008 0.001 ARG A 309 *********************** 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 100 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 48 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.2400 (mpp) cc_final: 0.0134 (tpp) REVERT: A 259 ILE cc_start: 0.2757 (OUTLIER) cc_final: 0.2192 (pp) REVERT: A 309 ARG cc_start: 0.2352 (OUTLIER) cc_final: 0.1321 (ptp-110) REVERT: A 347 GLU cc_start: 0.4782 (mm-30) cc_final: 0.4160 (pt0) REVERT: A 594 MET cc_start: 0.1689 (mmm) cc_final: 0.0851 (pmm) REVERT: A 697 ILE cc_start: 0.1529 (OUTLIER) cc_final: 0.1137 (mt) REVERT: A 698 ARG cc_start: 0.1991 (OUTLIER) cc_final: 0.1513 (mmp-170) REVERT: A 707 LEU cc_start: 0.1266 (OUTLIER) cc_final: 0.1013 (mt) REVERT: A 712 TYR cc_start: 0.0514 (OUTLIER) cc_final: -0.0165 (t80) REVERT: A 744 ASP cc_start: 0.1421 (OUTLIER) cc_final: 0.0793 (p0) REVERT: A 813 TRP cc_start: 0.0813 (OUTLIER) cc_final: -0.0408 (m-10) outliers start: 52 outliers final: 20 residues processed: 97 average time/residue: 0.9021 time to fit residues: 95.3443 Evaluate side-chains 69 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 41 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 301 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 473 VAL 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 697 ILE Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 744 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 924 SER Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.0570 chunk 30 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- 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 291 ASN ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1617 moved from start: 0.6885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7985 Z= 0.196 Angle : 0.666 14.685 10873 Z= 0.323 Chirality : 0.044 0.148 1155 Planarity : 0.005 0.056 1426 Dihedral : 6.521 89.452 1131 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.05 % Allowed : 29.68 % Favored : 66.27 % 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: -0.63 (0.36), residues: 169 sheet: -0.23 (0.33), residues: 230 loop : -1.39 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 521 HIS 0.012 0.001 HIS A 568 PHE 0.012 0.002 PHE A 611 TYR 0.017 0.002 TYR A 746 ARG 0.008 0.001 ARG A 461 *********************** 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 78 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 44 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.2488 (mpp) cc_final: 0.0325 (tpp) REVERT: A 259 ILE cc_start: 0.2610 (OUTLIER) cc_final: 0.2221 (pp) REVERT: A 310 ASP cc_start: 0.2112 (OUTLIER) cc_final: 0.1539 (m-30) REVERT: A 329 THR cc_start: 0.6289 (t) cc_final: 0.6083 (t) REVERT: A 347 GLU cc_start: 0.4921 (mm-30) cc_final: 0.4469 (pt0) REVERT: A 594 MET cc_start: 0.1707 (mmm) cc_final: 0.0860 (pmm) REVERT: A 615 TRP cc_start: -0.0211 (OUTLIER) cc_final: -0.0639 (p90) REVERT: A 628 ILE cc_start: 0.3680 (OUTLIER) cc_final: 0.3099 (mm) REVERT: A 697 ILE cc_start: 0.1356 (OUTLIER) cc_final: 0.0920 (mt) REVERT: A 698 ARG cc_start: 0.1785 (OUTLIER) cc_final: 0.1536 (mmp-170) REVERT: A 712 TYR cc_start: 0.0407 (OUTLIER) cc_final: -0.0161 (t80) REVERT: A 813 TRP cc_start: 0.0684 (OUTLIER) cc_final: -0.0273 (m-10) outliers start: 34 outliers final: 15 residues processed: 74 average time/residue: 0.8591 time to fit residues: 69.5672 Evaluate side-chains 66 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 43 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 ARG 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 310 ASP Chi-restraints excluded: chain A residue 352 ASP 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 628 ILE Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 180 HIS ** A 529 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 625 HIS ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 HIS ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2761 moved from start: 1.0307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.151 7985 Z= 0.443 Angle : 1.075 20.113 10873 Z= 0.541 Chirality : 0.059 0.297 1155 Planarity : 0.010 0.165 1426 Dihedral : 7.561 77.258 1130 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 31.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 5.24 % Allowed : 28.37 % Favored : 66.39 % 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: -2.63 (0.25), residues: 954 helix: -1.85 (0.31), residues: 174 sheet: -0.77 (0.34), residues: 211 loop : -2.17 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP A 687 HIS 0.017 0.003 HIS A 568 PHE 0.029 0.004 PHE A 845 TYR 0.037 0.004 TYR A 733 ARG 0.013 0.001 ARG A 817 *********************** 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 104 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 60 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 TRP cc_start: 0.3908 (m100) cc_final: 0.2794 (m100) REVERT: A 259 ILE cc_start: 0.3793 (OUTLIER) cc_final: 0.2868 (mt) REVERT: A 309 ARG cc_start: 0.4611 (OUTLIER) cc_final: 0.1931 (ptm160) REVERT: A 543 MET cc_start: 0.2343 (mtt) cc_final: 0.1471 (tpp) REVERT: A 628 ILE cc_start: 0.4454 (OUTLIER) cc_final: 0.4197 (mm) REVERT: A 697 ILE cc_start: 0.1626 (OUTLIER) cc_final: 0.1327 (mt) REVERT: A 712 TYR cc_start: 0.0903 (OUTLIER) cc_final: 0.0452 (t80) REVERT: A 726 MET cc_start: 0.3938 (OUTLIER) cc_final: 0.3496 (ttm) REVERT: A 774 GLU cc_start: 0.1985 (mt-10) cc_final: 0.1525 (tm-30) REVERT: A 813 TRP cc_start: 0.1573 (OUTLIER) cc_final: 0.0342 (m-10) outliers start: 44 outliers final: 11 residues processed: 96 average time/residue: 1.0175 time to fit residues: 105.5451 Evaluate side-chains 61 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 43 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 352 ASP 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 661 VAL Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 0.0970 chunk 84 optimal weight: 0.0970 chunk 88 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 GLN ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2687 moved from start: 1.0472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7985 Z= 0.217 Angle : 0.773 15.002 10873 Z= 0.378 Chirality : 0.047 0.187 1155 Planarity : 0.006 0.060 1426 Dihedral : 6.537 72.022 1127 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 3.10 % Allowed : 30.15 % Favored : 66.75 % 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: -2.05 (0.26), residues: 954 helix: -1.07 (0.35), residues: 168 sheet: -0.36 (0.36), residues: 214 loop : -1.93 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 730 HIS 0.007 0.001 HIS A 785 PHE 0.024 0.002 PHE A 611 TYR 0.017 0.002 TYR A 746 ARG 0.004 0.001 ARG A 460 *********************** 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: 26 poor density : 55 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.5146 (mttm) cc_final: 0.4889 (tptt) REVERT: A 142 MET cc_start: 0.3962 (OUTLIER) cc_final: 0.1519 (tpt) REVERT: A 226 TRP cc_start: 0.3373 (m100) cc_final: 0.2353 (m100) REVERT: A 250 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7093 (pt) REVERT: A 259 ILE cc_start: 0.3775 (OUTLIER) cc_final: 0.3163 (pp) REVERT: A 309 ARG cc_start: 0.4358 (OUTLIER) cc_final: 0.2087 (ptp-110) REVERT: A 524 MET cc_start: 0.1331 (tmm) cc_final: 0.0924 (ptt) REVERT: A 574 ILE cc_start: 0.1780 (OUTLIER) cc_final: 0.1435 (mm) REVERT: A 594 MET cc_start: 0.2057 (mmm) cc_final: 0.1572 (pp-130) REVERT: A 712 TYR cc_start: 0.0615 (OUTLIER) cc_final: 0.0320 (t80) REVERT: A 813 TRP cc_start: 0.1010 (OUTLIER) cc_final: 0.0348 (m-10) REVERT: A 912 GLU cc_start: 0.2486 (mm-30) cc_final: 0.1909 (tt0) outliers start: 26 outliers final: 7 residues processed: 74 average time/residue: 0.8343 time to fit residues: 67.6648 Evaluate side-chains 64 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 THR 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: 0.0170 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3002 moved from start: 1.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7985 Z= 0.257 Angle : 0.814 15.183 10873 Z= 0.396 Chirality : 0.049 0.173 1155 Planarity : 0.007 0.064 1426 Dihedral : 6.280 70.146 1127 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.22 % Allowed : 30.39 % Favored : 66.39 % 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: -2.04 (0.26), residues: 954 helix: -0.97 (0.36), residues: 168 sheet: -0.41 (0.36), residues: 208 loop : -1.90 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 813 HIS 0.031 0.002 HIS A 785 PHE 0.017 0.002 PHE A 611 TYR 0.020 0.002 TYR A 746 ARG 0.005 0.001 ARG A 460 *********************** 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 89 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 62 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.5333 (mttm) cc_final: 0.4968 (tptt) REVERT: A 142 MET cc_start: 0.4734 (OUTLIER) cc_final: 0.2292 (tpt) REVERT: A 310 ASP cc_start: 0.3930 (OUTLIER) cc_final: 0.3499 (m-30) REVERT: A 524 MET cc_start: 0.1652 (tmm) cc_final: 0.0512 (ptm) REVERT: A 574 ILE cc_start: 0.1531 (OUTLIER) cc_final: 0.1139 (mm) REVERT: A 594 MET cc_start: 0.2370 (mmm) cc_final: 0.2074 (pp-130) REVERT: A 712 TYR cc_start: 0.0751 (OUTLIER) cc_final: 0.0500 (t80) REVERT: A 730 TRP cc_start: 0.4188 (p-90) cc_final: 0.3828 (p-90) REVERT: A 813 TRP cc_start: 0.1093 (OUTLIER) cc_final: 0.0469 (m-10) REVERT: A 912 GLU cc_start: 0.2404 (OUTLIER) cc_final: 0.2020 (tt0) outliers start: 27 outliers final: 10 residues processed: 81 average time/residue: 0.9147 time to fit residues: 80.6945 Evaluate side-chains 67 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 615 TRP 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 743 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 912 GLU 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: 0.7980 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 0.0570 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 58 optimal weight: 0.0030 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 0.0270 chunk 81 optimal weight: 2.9990 overall best weight: 0.2166 ------------------------------------------------------------------------------- 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 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2970 moved from start: 1.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7985 Z= 0.204 Angle : 0.736 13.318 10873 Z= 0.354 Chirality : 0.045 0.175 1155 Planarity : 0.006 0.089 1426 Dihedral : 5.960 68.827 1127 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.71 % Favored : 93.19 % Rotamer: Outliers : 2.50 % Allowed : 31.70 % Favored : 65.79 % 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: -1.66 (0.26), residues: 954 helix: -0.46 (0.37), residues: 166 sheet: -0.29 (0.35), residues: 220 loop : -1.69 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 623 HIS 0.006 0.001 HIS A 262 PHE 0.017 0.002 PHE A 611 TYR 0.024 0.002 TYR A 746 ARG 0.012 0.001 ARG A 662 ********************** 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 80 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 59 time to evaluate : 0.855 Fit side-chains REVERT: A 96 LYS cc_start: 0.5332 (mttm) cc_final: 0.5088 (tmtt) REVERT: A 98 MET cc_start: 0.4022 (mmm) cc_final: 0.3438 (mmm) REVERT: A 142 MET cc_start: 0.4566 (OUTLIER) cc_final: 0.2194 (tpt) REVERT: A 269 LYS cc_start: 0.6828 (tppt) cc_final: 0.6353 (ttmt) REVERT: A 309 ARG cc_start: 0.4588 (tpt-90) cc_final: 0.2522 (ptp-110) REVERT: A 310 ASP cc_start: 0.4186 (m-30) cc_final: 0.3856 (m-30) REVERT: A 524 MET cc_start: 0.1688 (tmm) cc_final: 0.0678 (ptm) REVERT: A 543 MET cc_start: 0.2324 (mtt) cc_final: 0.1156 (tpp) REVERT: A 615 TRP cc_start: -0.0880 (OUTLIER) cc_final: -0.1428 (p90) REVERT: A 632 MET cc_start: 0.1709 (ttt) cc_final: -0.0771 (mpt) REVERT: A 730 TRP cc_start: 0.3791 (p-90) cc_final: 0.3346 (p-90) REVERT: A 813 TRP cc_start: 0.0853 (OUTLIER) cc_final: 0.0087 (m-90) REVERT: A 912 GLU cc_start: 0.2062 (OUTLIER) cc_final: 0.1796 (tt0) outliers start: 21 outliers final: 7 residues processed: 74 average time/residue: 0.9205 time to fit residues: 74.3631 Evaluate side-chains 64 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 912 GLU 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: 1.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.0020 chunk 76 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 50 GLN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 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 = 0.5006 r_free = 0.5006 target = 0.286406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.272170 restraints weight = 9625.398| |-----------------------------------------------------------------------------| r_work (start): 0.4929 rms_B_bonded: 1.56 r_work: 0.4870 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4789 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3590 moved from start: 1.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 7985 Z= 0.284 Angle : 0.842 12.427 10873 Z= 0.418 Chirality : 0.050 0.327 1155 Planarity : 0.007 0.060 1426 Dihedral : 6.194 61.012 1127 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.91 % Favored : 90.99 % Rotamer: Outliers : 2.38 % Allowed : 32.06 % Favored : 65.55 % 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: -0.67 (0.37), residues: 162 sheet: -0.42 (0.35), residues: 221 loop : -1.71 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 355 HIS 0.013 0.002 HIS A 568 PHE 0.019 0.002 PHE A 178 TYR 0.028 0.002 TYR A 712 ARG 0.017 0.001 ARG A 662 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2760.85 seconds wall clock time: 50 minutes 6.64 seconds (3006.64 seconds total)