Starting phenix.real_space_refine on Tue Sep 24 11:54:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/09_2024/8d43_27173.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/09_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_27173/09_2024/8d43_27173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/09_2024/8d43_27173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/09_2024/8d43_27173.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d43_27173/09_2024/8d43_27173.cif" } 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. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.52, per 1000 atoms: 0.71 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 2.20 Conformation dependent library (CDL) restraints added in 920.4 milliseconds 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: 1.12 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: 3.05 Time building geometry restraints manager: 2.53 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: 0.00 - 2.19: 10547 2.19 - 4.38: 281 4.38 - 6.58: 31 6.58 - 8.77: 11 8.77 - 10.96: 3 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 Time spend for trying shortcut: 0.00 ========== 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.800 Find NCS groups from input model: 0.080 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.560 ------------------------------------------------------------------------------- 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 : 0.746 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: 0.8425 time to fit residues: 101.1022 Evaluate side-chains 53 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 36 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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: 0.4980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.0828 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 7985 Z= 0.339 Angle : 0.882 15.943 10873 Z= 0.439 Chirality : 0.053 0.207 1155 Planarity : 0.008 0.082 1426 Dihedral : 10.151 79.858 1170 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 8.22 % Allowed : 22.41 % Favored : 69.37 % 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 (0.27), residues: 954 helix: -1.06 (0.35), residues: 168 sheet: -0.45 (0.32), residues: 239 loop : -1.18 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A 315 HIS 0.013 0.003 HIS A 572 PHE 0.020 0.003 PHE A 845 TYR 0.023 0.003 TYR A 438 ARG 0.014 0.001 ARG A 493 *********************** 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 115 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 46 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: -0.1171 (OUTLIER) cc_final: -0.1516 (tp) REVERT: A 259 ILE cc_start: 0.2267 (OUTLIER) cc_final: 0.0966 (mp) REVERT: A 591 SER cc_start: -0.1950 (OUTLIER) cc_final: -0.2461 (t) REVERT: A 615 TRP cc_start: 0.0618 (OUTLIER) cc_final: -0.0130 (p90) REVERT: A 635 SER cc_start: 0.0929 (OUTLIER) cc_final: -0.0016 (t) REVERT: A 656 GLU cc_start: 0.0143 (OUTLIER) cc_final: -0.2309 (mm-30) REVERT: A 699 ASP cc_start: -0.0194 (OUTLIER) cc_final: -0.0398 (t70) REVERT: A 745 GLN cc_start: -0.0995 (OUTLIER) cc_final: -0.1676 (mt0) REVERT: A 814 MET cc_start: 0.1534 (mmt) cc_final: -0.2332 (tpp) REVERT: A 880 GLU cc_start: -0.0586 (OUTLIER) cc_final: -0.0806 (pt0) outliers start: 69 outliers final: 21 residues processed: 107 average time/residue: 0.9624 time to fit residues: 111.5212 Evaluate side-chains 72 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 42 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG 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 259 ILE Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 591 SER 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 697 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 707 LEU 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 880 GLU 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: 2.9990 chunk 27 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 0.0770 chunk 87 optimal weight: 0.2980 chunk 94 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 670 GLN A 676 HIS A 785 HIS B 29 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0939 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7985 Z= 0.221 Angle : 0.682 10.261 10873 Z= 0.336 Chirality : 0.046 0.176 1155 Planarity : 0.006 0.057 1426 Dihedral : 8.043 85.301 1153 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.29 % Allowed : 25.74 % Favored : 69.96 % 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: -1.39 (0.26), residues: 954 helix: -0.69 (0.35), residues: 165 sheet: -0.52 (0.33), residues: 234 loop : -1.15 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 730 HIS 0.008 0.002 HIS A 572 PHE 0.022 0.002 PHE A 46 TYR 0.015 0.002 TYR A 669 ARG 0.011 0.001 ARG A 173 *********************** 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 76 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 40 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 ILE cc_start: 0.2405 (pt) cc_final: 0.1515 (mp) REVERT: A 615 TRP cc_start: 0.0124 (OUTLIER) cc_final: -0.0256 (p90) REVERT: A 635 SER cc_start: 0.0912 (OUTLIER) cc_final: 0.0046 (m) REVERT: A 656 GLU cc_start: 0.0559 (OUTLIER) cc_final: -0.1093 (tm-30) REVERT: A 814 MET cc_start: 0.2005 (mmt) cc_final: -0.2312 (tpp) outliers start: 36 outliers final: 15 residues processed: 71 average time/residue: 0.9134 time to fit residues: 70.8834 Evaluate side-chains 54 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 36 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 256 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 543 MET 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 779 ILE Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 29 HIS 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: 0.0270 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 0.0070 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.0570 chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1056 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7985 Z= 0.188 Angle : 0.681 14.710 10873 Z= 0.327 Chirality : 0.045 0.192 1155 Planarity : 0.006 0.056 1426 Dihedral : 7.403 88.317 1152 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 4.17 % Allowed : 26.70 % 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: -1.14 (0.27), residues: 954 helix: -0.35 (0.37), residues: 164 sheet: -0.30 (0.33), residues: 237 loop : -1.08 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 322 HIS 0.033 0.002 HIS B 29 PHE 0.017 0.002 PHE A 46 TYR 0.014 0.002 TYR A 746 ARG 0.008 0.001 ARG A 164 *********************** 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 74 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 39 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.4563 (mm-30) cc_final: 0.3723 (pt0) REVERT: A 615 TRP cc_start: 0.0000 (OUTLIER) cc_final: -0.0556 (p90) REVERT: A 635 SER cc_start: 0.0980 (OUTLIER) cc_final: 0.0036 (t) REVERT: A 712 TYR cc_start: 0.0285 (OUTLIER) cc_final: -0.0250 (t80) REVERT: A 726 MET cc_start: 0.2626 (mtt) cc_final: 0.2264 (ptm) outliers start: 35 outliers final: 14 residues processed: 69 average time/residue: 0.8780 time to fit residues: 66.4275 Evaluate side-chains 52 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 35 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 76 VAL 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 301 VAL 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 635 SER Chi-restraints excluded: chain A residue 687 TRP 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 935 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.0000 chunk 0 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 804 GLN A 850 HIS ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1871 moved from start: 0.7314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 7985 Z= 0.341 Angle : 0.935 23.674 10873 Z= 0.452 Chirality : 0.053 0.309 1155 Planarity : 0.008 0.073 1426 Dihedral : 7.648 82.203 1152 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 5.72 % Allowed : 26.22 % 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: -1.94 (0.26), residues: 954 helix: -1.26 (0.36), residues: 173 sheet: -0.65 (0.34), residues: 226 loop : -1.59 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 355 HIS 0.010 0.002 HIS A 572 PHE 0.032 0.003 PHE A 845 TYR 0.032 0.003 TYR A 578 ARG 0.011 0.001 ARG A 164 *********************** 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 101 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 53 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 TYR cc_start: 0.4422 (m-80) cc_final: 0.4182 (m-80) REVERT: A 76 VAL cc_start: 0.3055 (OUTLIER) cc_final: 0.1884 (m) REVERT: A 142 MET cc_start: 0.2946 (mpp) cc_final: 0.0864 (tpt) REVERT: A 250 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5721 (pp) REVERT: A 347 GLU cc_start: 0.4991 (mm-30) cc_final: 0.4636 (pt0) REVERT: A 543 MET cc_start: 0.1678 (OUTLIER) cc_final: 0.1291 (mpp) REVERT: A 609 GLN cc_start: 0.2676 (OUTLIER) cc_final: 0.1837 (mp10) REVERT: A 712 TYR cc_start: 0.0364 (OUTLIER) cc_final: -0.0056 (t80) REVERT: A 726 MET cc_start: 0.2440 (mtt) cc_final: 0.2117 (ptm) REVERT: A 823 MET cc_start: 0.4202 (tmt) cc_final: 0.3914 (tmt) outliers start: 48 outliers final: 20 residues processed: 94 average time/residue: 0.7443 time to fit residues: 77.3628 Evaluate side-chains 69 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 44 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 580 HIS 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 661 VAL 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 785 HIS Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 ARG 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: 0.5980 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.0980 chunk 92 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1833 moved from start: 0.7639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7985 Z= 0.203 Angle : 0.700 12.690 10873 Z= 0.341 Chirality : 0.046 0.191 1155 Planarity : 0.006 0.059 1426 Dihedral : 6.682 75.658 1148 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % 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: -1.57 (0.27), residues: 954 helix: -0.73 (0.37), residues: 167 sheet: -0.30 (0.34), residues: 229 loop : -1.48 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 501 HIS 0.014 0.001 HIS A 568 PHE 0.015 0.002 PHE A 611 TYR 0.033 0.002 TYR A 578 ARG 0.010 0.001 ARG A 49 *********************** 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 76 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 44 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.4081 (t) cc_final: 0.3769 (t) REVERT: A 74 LEU cc_start: 0.1718 (OUTLIER) cc_final: 0.1361 (tt) REVERT: A 76 VAL cc_start: 0.3157 (OUTLIER) cc_final: 0.2014 (m) REVERT: A 250 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5970 (pp) REVERT: A 259 ILE cc_start: 0.3728 (OUTLIER) cc_final: 0.3266 (pp) REVERT: A 347 GLU cc_start: 0.4885 (mm-30) cc_final: 0.4600 (pt0) REVERT: A 543 MET cc_start: 0.1619 (OUTLIER) cc_final: 0.0890 (mpp) REVERT: A 687 TRP cc_start: -0.0203 (OUTLIER) cc_final: -0.1115 (p-90) REVERT: A 697 ILE cc_start: 0.1368 (OUTLIER) cc_final: 0.1041 (mt) REVERT: A 712 TYR cc_start: 0.0498 (OUTLIER) cc_final: -0.0103 (t80) REVERT: A 823 MET cc_start: 0.4204 (tmt) cc_final: 0.3973 (tmt) outliers start: 32 outliers final: 13 residues processed: 71 average time/residue: 0.7268 time to fit residues: 57.3371 Evaluate side-chains 61 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 40 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 76 VAL 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 299 VAL Chi-restraints excluded: chain A residue 470 HIS 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 635 SER Chi-restraints excluded: chain A residue 661 VAL 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 779 ILE Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 ARG 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: 0.7980 chunk 67 optimal weight: 0.0980 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN A 573 ASN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 GLN A 855 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2280 moved from start: 0.8940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7985 Z= 0.275 Angle : 0.793 17.720 10873 Z= 0.389 Chirality : 0.049 0.241 1155 Planarity : 0.006 0.062 1426 Dihedral : 6.661 64.475 1148 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.29 % Allowed : 27.53 % Favored : 68.18 % 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: -1.80 (0.26), residues: 954 helix: -0.86 (0.36), residues: 167 sheet: -0.53 (0.34), residues: 219 loop : -1.60 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP A 730 HIS 0.010 0.002 HIS A 568 PHE 0.027 0.003 PHE A 611 TYR 0.020 0.003 TYR A 669 ARG 0.006 0.001 ARG A 49 *********************** 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 85 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 49 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 TYR cc_start: 0.6580 (m-80) cc_final: 0.6349 (m-80) REVERT: A 142 MET cc_start: 0.3668 (OUTLIER) cc_final: 0.1251 (tpt) REVERT: A 226 TRP cc_start: 0.2326 (m-90) cc_final: 0.1066 (m-90) REVERT: A 259 ILE cc_start: 0.3391 (OUTLIER) cc_final: 0.2654 (pp) REVERT: A 524 MET cc_start: 0.1009 (tmm) cc_final: 0.0484 (ptm) REVERT: A 543 MET cc_start: 0.1783 (OUTLIER) cc_final: 0.0960 (mpp) REVERT: A 697 ILE cc_start: 0.1481 (OUTLIER) cc_final: 0.1139 (mt) REVERT: A 712 TYR cc_start: 0.0656 (OUTLIER) cc_final: 0.0052 (t80) REVERT: A 823 MET cc_start: 0.4180 (tmt) cc_final: 0.3966 (tmt) outliers start: 36 outliers final: 16 residues processed: 78 average time/residue: 0.7332 time to fit residues: 63.8083 Evaluate side-chains 66 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 45 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 137 SER 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 299 VAL Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 661 VAL 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 708 LEU Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain B residue 30 PHE 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: 0.0870 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 84 optimal weight: 0.0270 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.0070 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS A 772 GLN A 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2269 moved from start: 0.9323 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= 0.190 Angle : 0.715 12.235 10873 Z= 0.346 Chirality : 0.046 0.250 1155 Planarity : 0.006 0.062 1426 Dihedral : 5.999 60.138 1147 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.74 % Allowed : 28.84 % Favored : 68.41 % 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: -1.77 (0.26), residues: 954 helix: -0.66 (0.37), residues: 172 sheet: -0.48 (0.33), residues: 226 loop : -1.68 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 501 HIS 0.006 0.001 HIS A 755 PHE 0.048 0.002 PHE A 101 TYR 0.014 0.002 TYR A 669 ARG 0.007 0.000 ARG A 602 *********************** 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 67 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 44 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.5135 (mm-30) cc_final: 0.4871 (tt0) REVERT: A 74 LEU cc_start: 0.1875 (OUTLIER) cc_final: 0.1364 (tt) REVERT: A 142 MET cc_start: 0.3527 (OUTLIER) cc_final: 0.1241 (tpt) REVERT: A 226 TRP cc_start: 0.2583 (m-90) cc_final: 0.1559 (m-90) REVERT: A 259 ILE cc_start: 0.3172 (OUTLIER) cc_final: 0.2836 (mt) REVERT: A 405 ASP cc_start: 0.1253 (p0) cc_final: 0.1026 (p0) REVERT: A 524 MET cc_start: 0.0962 (tmm) cc_final: 0.0497 (ptm) REVERT: A 543 MET cc_start: 0.1624 (OUTLIER) cc_final: 0.1102 (mpp) REVERT: A 712 TYR cc_start: 0.0550 (OUTLIER) cc_final: 0.0039 (t80) outliers start: 23 outliers final: 12 residues processed: 61 average time/residue: 0.8194 time to fit residues: 55.2731 Evaluate side-chains 60 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 51 optimal weight: 0.2980 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN A 783 GLN A 850 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2768 moved from start: 1.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 7985 Z= 0.285 Angle : 0.776 10.623 10873 Z= 0.393 Chirality : 0.049 0.243 1155 Planarity : 0.007 0.060 1426 Dihedral : 5.974 54.443 1147 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 1.79 % Allowed : 29.68 % Favored : 68.53 % 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: -1.91 (0.26), residues: 954 helix: -1.03 (0.35), residues: 174 sheet: -0.49 (0.34), residues: 222 loop : -1.71 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 501 HIS 0.010 0.002 HIS A 470 PHE 0.032 0.002 PHE A 101 TYR 0.047 0.003 TYR A 509 ARG 0.006 0.001 ARG A 590 *********************** 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 75 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.4994 (mttm) cc_final: 0.4715 (tptt) REVERT: A 142 MET cc_start: 0.4393 (OUTLIER) cc_final: 0.1879 (tpt) REVERT: A 226 TRP cc_start: 0.3522 (m-90) cc_final: 0.2793 (m-90) REVERT: A 242 MET cc_start: 0.4931 (mmm) cc_final: 0.4417 (mmm) REVERT: A 322 TRP cc_start: 0.3887 (m100) cc_final: 0.3428 (m100) REVERT: A 524 MET cc_start: 0.1297 (tmm) cc_final: 0.0770 (ptm) REVERT: A 670 GLN cc_start: 0.0413 (OUTLIER) cc_final: -0.0311 (pt0) REVERT: A 740 PHE cc_start: 0.5459 (m-10) cc_final: 0.5050 (m-80) outliers start: 15 outliers final: 8 residues processed: 71 average time/residue: 0.9601 time to fit residues: 74.0744 Evaluate side-chains 58 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.0770 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 88 optimal weight: 0.1980 chunk 76 optimal weight: 0.4980 chunk 7 optimal weight: 0.0670 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 chunk 81 optimal weight: 0.7980 overall best weight: 0.1874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2714 moved from start: 1.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 7985 Z= 0.202 Angle : 0.694 10.397 10873 Z= 0.340 Chirality : 0.046 0.263 1155 Planarity : 0.006 0.059 1426 Dihedral : 5.704 55.051 1146 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.31 % Allowed : 30.75 % 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: -1.75 (0.26), residues: 954 helix: -0.61 (0.37), residues: 168 sheet: -0.44 (0.33), residues: 226 loop : -1.69 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 501 HIS 0.006 0.001 HIS A 568 PHE 0.039 0.002 PHE A 101 TYR 0.019 0.002 TYR A 669 ARG 0.006 0.000 ARG A 602 ********************** 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 65 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.1955 (OUTLIER) cc_final: 0.1540 (tp) REVERT: A 96 LYS cc_start: 0.4875 (mttm) cc_final: 0.4558 (tptt) REVERT: A 142 MET cc_start: 0.4444 (OUTLIER) cc_final: 0.1982 (tpt) REVERT: A 226 TRP cc_start: 0.3252 (m-90) cc_final: 0.2384 (m-90) REVERT: A 242 MET cc_start: 0.4679 (mmm) cc_final: 0.4317 (mmm) REVERT: A 259 ILE cc_start: 0.3354 (mt) cc_final: 0.3025 (mp) REVERT: A 322 TRP cc_start: 0.3742 (m100) cc_final: 0.2958 (m100) REVERT: A 524 MET cc_start: 0.1030 (tmm) cc_final: 0.0790 (ptm) REVERT: A 543 MET cc_start: 0.1346 (tpp) cc_final: -0.0299 (mtm) REVERT: A 740 PHE cc_start: 0.5720 (m-10) cc_final: 0.5329 (m-80) outliers start: 11 outliers final: 8 residues processed: 62 average time/residue: 0.9447 time to fit residues: 63.9653 Evaluate side-chains 59 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 687 TRP Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.0270 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 66 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 HIS ** 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 = 0.4850 r_free = 0.4850 target = 0.275025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.260977 restraints weight = 9575.740| |-----------------------------------------------------------------------------| r_work (start): 0.4736 rms_B_bonded: 1.59 r_work: 0.4687 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4600 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3379 moved from start: 1.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7985 Z= 0.261 Angle : 0.821 14.592 10873 Z= 0.409 Chirality : 0.050 0.251 1155 Planarity : 0.007 0.065 1426 Dihedral : 5.975 51.528 1146 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.15 % Allowed : 30.51 % Favored : 67.34 % 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: -1.89 (0.25), residues: 954 helix: -0.92 (0.36), residues: 174 sheet: -0.54 (0.33), residues: 224 loop : -1.71 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 663 HIS 0.010 0.001 HIS A 568 PHE 0.031 0.002 PHE A 101 TYR 0.022 0.002 TYR A 746 ARG 0.028 0.001 ARG A 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2677.67 seconds wall clock time: 47 minutes 53.86 seconds (2873.86 seconds total)