Starting phenix.real_space_refine on Sat Jul 20 01:10:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/07_2024/8t6u_41081.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/07_2024/8t6u_41081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/07_2024/8t6u_41081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/07_2024/8t6u_41081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/07_2024/8t6u_41081.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6u_41081/07_2024/8t6u_41081.cif" } resolution = 3.13 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= -0.003 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 5826 2.51 5 N 1328 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 681": "OE1" <-> "OE2" Residue "B GLU 777": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8638 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4071 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4071 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 256 Unusual residues: {'CLR': 4, 'H9F': 1, 'PC1': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 148 Unusual residues: {'CLR': 4, 'H9F': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Time building chain proxies: 5.55, per 1000 atoms: 0.64 Number of scatterers: 8638 At special positions: 0 Unit cell: (72.092, 132.348, 83.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 2 15.00 O 1446 8.00 N 1328 7.00 C 5826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG D 1 " - " ASN A 642 " " NAG L 1 " - " ASN B 642 " Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 73.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 379 through 390 removed outlier: 3.515A pdb=" N VAL A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.709A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 485 through 507 removed outlier: 3.521A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 515 Processing helix chain 'A' and resid 517 through 547 Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.580A pdb=" N LEU A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.535A pdb=" N ILE A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 667 Processing helix chain 'A' and resid 667 through 690 Processing helix chain 'A' and resid 701 through 717 removed outlier: 3.692A pdb=" N ASP A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 706 " --> pdb=" O PHE A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 727 through 738 Processing helix chain 'A' and resid 760 through 772 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 784 through 799 removed outlier: 3.974A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 858 through 865 removed outlier: 3.553A pdb=" N LEU A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 873 removed outlier: 3.534A pdb=" N ARG A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.821A pdb=" N ILE A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 Processing helix chain 'B' and resid 379 through 390 removed outlier: 3.513A pdb=" N VAL B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.706A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 485 through 507 removed outlier: 3.520A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 Processing helix chain 'B' and resid 517 through 547 Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.581A pdb=" N LEU B 573 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.536A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 667 Processing helix chain 'B' and resid 667 through 690 Processing helix chain 'B' and resid 701 through 717 removed outlier: 3.690A pdb=" N ASP B 705 " --> pdb=" O GLY B 701 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 720 No H-bonds generated for 'chain 'B' and resid 718 through 720' Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 760 through 772 Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 799 removed outlier: 3.974A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 812 Processing helix chain 'B' and resid 822 through 828 Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 858 through 865 removed outlier: 3.554A pdb=" N LEU B 865 " --> pdb=" O PHE B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 873 removed outlier: 3.533A pdb=" N ARG B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 878 removed outlier: 3.827A pdb=" N ILE B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742 removed outlier: 7.366A pdb=" N VAL A 740 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 754 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 752 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742 removed outlier: 7.365A pdb=" N VAL B 740 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 754 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 752 " --> pdb=" O GLY B 742 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 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: 1.20 - 1.32: 1333 1.32 - 1.45: 2348 1.45 - 1.58: 5084 1.58 - 1.71: 5 1.71 - 1.84: 66 Bond restraints: 8836 Sorted by residual: bond pdb=" C5 H9F B2203 " pdb=" N8 H9F B2203 " ideal model delta sigma weight residual 1.348 1.508 -0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" C5 H9F A2204 " pdb=" N8 H9F A2204 " ideal model delta sigma weight residual 1.348 1.487 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C2 H9F B2203 " pdb=" N7 H9F B2203 " ideal model delta sigma weight residual 1.360 1.490 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C2 H9F A2204 " pdb=" N7 H9F A2204 " ideal model delta sigma weight residual 1.360 1.482 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C6 H9F B2203 " pdb=" N6 H9F B2203 " ideal model delta sigma weight residual 1.364 1.471 -0.107 2.00e-02 2.50e+03 2.86e+01 ... (remaining 8831 not shown) Histogram of bond angle deviations from ideal: 95.40 - 103.26: 100 103.26 - 111.12: 3099 111.12 - 118.98: 4451 118.98 - 126.84: 4315 126.84 - 134.70: 71 Bond angle restraints: 12036 Sorted by residual: angle pdb=" C ILE B 493 " pdb=" N GLY B 494 " pdb=" CA GLY B 494 " ideal model delta sigma weight residual 119.98 125.48 -5.50 1.11e+00 8.12e-01 2.45e+01 angle pdb=" C ILE A 493 " pdb=" N GLY A 494 " pdb=" CA GLY A 494 " ideal model delta sigma weight residual 119.98 125.42 -5.44 1.11e+00 8.12e-01 2.41e+01 angle pdb=" N GLN A 434 " pdb=" CA GLN A 434 " pdb=" C GLN A 434 " ideal model delta sigma weight residual 111.28 106.09 5.19 1.09e+00 8.42e-01 2.27e+01 angle pdb=" N PRO A 722 " pdb=" CA PRO A 722 " pdb=" C PRO A 722 " ideal model delta sigma weight residual 110.55 117.88 -7.33 1.63e+00 3.76e-01 2.02e+01 angle pdb=" N PRO B 722 " pdb=" CA PRO B 722 " pdb=" C PRO B 722 " ideal model delta sigma weight residual 110.55 117.72 -7.17 1.63e+00 3.76e-01 1.94e+01 ... (remaining 12031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 5507 34.06 - 68.12: 167 68.12 - 102.18: 16 102.18 - 136.24: 3 136.24 - 170.30: 1 Dihedral angle restraints: 5694 sinusoidal: 2718 harmonic: 2976 Sorted by residual: dihedral pdb=" C18 H9F A2204 " pdb=" C19 H9F A2204 " pdb=" N7 H9F A2204 " pdb=" C2 H9F A2204 " ideal model delta sinusoidal sigma weight residual 90.87 -98.83 -170.30 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C17 H9F A2204 " pdb=" C18 H9F A2204 " pdb=" C19 H9F A2204 " pdb=" N7 H9F A2204 " ideal model delta sinusoidal sigma weight residual 55.70 -69.79 125.49 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C21 H9F B2203 " pdb=" C22 H9F B2203 " pdb=" C23 H9F B2203 " pdb=" C24 H9F B2203 " ideal model delta sinusoidal sigma weight residual -64.51 52.53 -117.04 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 5691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.848: 1434 0.848 - 1.697: 0 1.697 - 2.545: 0 2.545 - 3.393: 0 3.393 - 4.241: 2 Chirality restraints: 1436 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 1.84 -4.24 2.00e-02 2.50e+03 4.50e+04 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 1.83 -4.23 2.00e-02 2.50e+03 4.48e+04 chirality pdb=" CB ILE A 493 " pdb=" CA ILE A 493 " pdb=" CG1 ILE A 493 " pdb=" CG2 ILE A 493 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1433 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.072 2.00e-02 2.50e+03 6.31e-02 4.98e+01 pdb=" C7 NAG D 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.085 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.068 2.00e-02 2.50e+03 5.99e-02 4.48e+01 pdb=" C7 NAG L 1 " 0.054 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.062 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.081 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 878 " -0.042 2.00e-02 2.50e+03 3.28e-02 1.88e+01 pdb=" CG PHE A 878 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 878 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 878 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 PHE A 878 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 878 " -0.038 2.00e-02 2.50e+03 pdb=" CZ PHE A 878 " -0.020 2.00e-02 2.50e+03 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 895 2.78 - 3.31: 9182 3.31 - 3.84: 14079 3.84 - 4.37: 18538 4.37 - 4.90: 30013 Nonbonded interactions: 72707 Sorted by model distance: nonbonded pdb=" OH TYR A 555 " pdb=" OH TYR B 555 " model vdw 2.246 2.440 nonbonded pdb=" NH2 ARG A 646 " pdb=" CA GLY A 720 " model vdw 2.373 3.520 nonbonded pdb=" NH2 ARG A 879 " pdb=" OE2 GLU A 882 " model vdw 2.403 2.520 nonbonded pdb=" NH2 ARG B 879 " pdb=" OE2 GLU B 882 " model vdw 2.417 2.520 nonbonded pdb=" OG1 THR B 739 " pdb=" O HOH B2301 " model vdw 2.449 2.440 ... (remaining 72702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 369 through 891 or resid 2201 through 2202 or resid 2205)) \ selection = (chain 'B' and (resid 369 through 891 or resid 2201 through 2202 or resid 2205)) \ } ncs_group { reference = chain 'D' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.360 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 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 : 0.011 0.160 8836 Z= 0.728 Angle : 1.485 7.330 12036 Z= 1.025 Chirality : 0.175 4.241 1436 Planarity : 0.009 0.096 1404 Dihedral : 15.188 170.302 3774 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.64 % Favored : 97.17 % Rotamer: Outliers : 0.33 % Allowed : 5.02 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.20), residues: 1024 helix: -1.70 (0.15), residues: 704 sheet: None (None), residues: 0 loop : -2.66 (0.27), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.009 TRP B 723 HIS 0.018 0.006 HIS B 819 PHE 0.053 0.007 PHE A 878 TYR 0.036 0.009 TYR A 596 ARG 0.014 0.003 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 406 LEU cc_start: 0.9412 (tt) cc_final: 0.9208 (tp) REVERT: A 554 ASN cc_start: 0.8690 (t0) cc_final: 0.8470 (t0) REVERT: B 406 LEU cc_start: 0.9404 (tt) cc_final: 0.9197 (tp) REVERT: B 554 ASN cc_start: 0.8692 (t0) cc_final: 0.8476 (t0) REVERT: B 712 MET cc_start: 0.8731 (mtm) cc_final: 0.8526 (mtm) outliers start: 3 outliers final: 3 residues processed: 135 average time/residue: 0.2320 time to fit residues: 42.2838 Evaluate side-chains 65 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 825 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8672 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8836 Z= 0.217 Angle : 0.588 6.687 12036 Z= 0.291 Chirality : 0.039 0.135 1436 Planarity : 0.005 0.049 1404 Dihedral : 12.271 149.606 1877 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.23 % Allowed : 9.82 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1024 helix: 1.05 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -1.71 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 831 HIS 0.002 0.001 HIS B 734 PHE 0.023 0.001 PHE A 411 TYR 0.010 0.002 TYR B 818 ARG 0.004 0.001 ARG B 656 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 68 time to evaluate : 0.994 Fit side-chains REVERT: B 406 LEU cc_start: 0.9395 (tt) cc_final: 0.9194 (tp) outliers start: 20 outliers final: 11 residues processed: 76 average time/residue: 0.1797 time to fit residues: 20.4878 Evaluate side-chains 69 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.0050 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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: 0.8685 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8836 Z= 0.189 Angle : 0.531 7.536 12036 Z= 0.260 Chirality : 0.038 0.146 1436 Planarity : 0.005 0.052 1404 Dihedral : 11.449 139.482 1875 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.34 % Allowed : 10.71 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1024 helix: 1.72 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.37 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 831 HIS 0.002 0.001 HIS A 734 PHE 0.015 0.001 PHE A 411 TYR 0.016 0.001 TYR B 818 ARG 0.005 0.001 ARG B 879 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 1.023 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 73 average time/residue: 0.1801 time to fit residues: 19.7319 Evaluate side-chains 65 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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: 0.8707 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8836 Z= 0.224 Angle : 0.532 5.785 12036 Z= 0.258 Chirality : 0.038 0.144 1436 Planarity : 0.005 0.053 1404 Dihedral : 10.635 130.415 1875 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.57 % Allowed : 10.16 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1024 helix: 1.83 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.22 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 831 HIS 0.001 0.001 HIS B 819 PHE 0.012 0.001 PHE B 411 TYR 0.017 0.001 TYR A 824 ARG 0.004 0.000 ARG B 879 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 55 time to evaluate : 0.974 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 66 average time/residue: 0.1855 time to fit residues: 18.3369 Evaluate side-chains 67 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8703 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8836 Z= 0.184 Angle : 0.515 6.397 12036 Z= 0.250 Chirality : 0.038 0.136 1436 Planarity : 0.005 0.053 1404 Dihedral : 10.167 120.320 1875 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.46 % Allowed : 10.27 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.26), residues: 1024 helix: 1.96 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.05 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 831 HIS 0.001 0.001 HIS B 819 PHE 0.012 0.001 PHE B 411 TYR 0.014 0.001 TYR A 824 ARG 0.003 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 0.962 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 68 average time/residue: 0.1840 time to fit residues: 18.8203 Evaluate side-chains 64 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 0.0570 chunk 56 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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: 0.8697 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8836 Z= 0.165 Angle : 0.521 8.280 12036 Z= 0.247 Chirality : 0.038 0.137 1436 Planarity : 0.005 0.052 1404 Dihedral : 9.617 103.885 1874 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.12 % Allowed : 11.16 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.27), residues: 1024 helix: 2.02 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.98 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 831 HIS 0.001 0.000 HIS B 819 PHE 0.012 0.001 PHE A 411 TYR 0.016 0.001 TYR B 824 ARG 0.004 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 1.069 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 72 average time/residue: 0.1846 time to fit residues: 20.1355 Evaluate side-chains 65 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8709 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8836 Z= 0.200 Angle : 0.545 7.487 12036 Z= 0.259 Chirality : 0.038 0.150 1436 Planarity : 0.005 0.052 1404 Dihedral : 9.063 87.069 1874 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.01 % Allowed : 11.27 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.27), residues: 1024 helix: 2.00 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.81 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 831 HIS 0.001 0.001 HIS B 819 PHE 0.010 0.001 PHE A 411 TYR 0.014 0.001 TYR A 824 ARG 0.003 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 1.034 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 62 average time/residue: 0.1902 time to fit residues: 17.6771 Evaluate side-chains 64 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.0010 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.4706 ------------------------------------------------------------------------------- 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: 0.8691 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8836 Z= 0.159 Angle : 0.547 8.772 12036 Z= 0.256 Chirality : 0.039 0.257 1436 Planarity : 0.005 0.052 1404 Dihedral : 8.836 87.206 1874 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.90 % Allowed : 11.72 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.27), residues: 1024 helix: 1.99 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.71 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 831 HIS 0.001 0.000 HIS B 819 PHE 0.011 0.001 PHE A 411 TYR 0.014 0.001 TYR A 824 ARG 0.004 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.994 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 64 average time/residue: 0.1884 time to fit residues: 18.1629 Evaluate side-chains 66 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 0.0470 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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: 0.8692 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8836 Z= 0.162 Angle : 0.546 8.709 12036 Z= 0.256 Chirality : 0.039 0.264 1436 Planarity : 0.005 0.053 1404 Dihedral : 8.659 86.898 1874 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.56 % Allowed : 12.39 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.27), residues: 1024 helix: 2.00 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.64 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 492 HIS 0.001 0.000 HIS B 547 PHE 0.010 0.001 PHE A 411 TYR 0.014 0.001 TYR A 824 ARG 0.007 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 1.023 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 59 average time/residue: 0.1971 time to fit residues: 17.3922 Evaluate side-chains 64 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 86 optimal weight: 0.0060 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- 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: 0.8710 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8836 Z= 0.204 Angle : 0.566 9.102 12036 Z= 0.266 Chirality : 0.039 0.304 1436 Planarity : 0.005 0.053 1404 Dihedral : 8.503 86.712 1874 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.67 % Allowed : 12.28 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.27), residues: 1024 helix: 2.09 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.28 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 492 HIS 0.001 0.000 HIS A 547 PHE 0.009 0.001 PHE A 411 TYR 0.014 0.001 TYR A 824 ARG 0.007 0.000 ARG A 603 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 1.027 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 61 average time/residue: 0.2034 time to fit residues: 18.5638 Evaluate side-chains 67 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.072195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.061353 restraints weight = 25281.002| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.95 r_work: 0.2848 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8836 Z= 0.182 Angle : 0.561 9.148 12036 Z= 0.262 Chirality : 0.038 0.156 1436 Planarity : 0.005 0.053 1404 Dihedral : 8.331 86.996 1874 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.56 % Allowed : 12.17 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.27), residues: 1024 helix: 2.08 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.17 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 831 HIS 0.001 0.000 HIS B 819 PHE 0.010 0.001 PHE A 411 TYR 0.014 0.001 TYR A 824 ARG 0.012 0.001 ARG B 603 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1718.98 seconds wall clock time: 31 minutes 42.20 seconds (1902.20 seconds total)