Starting phenix.real_space_refine on Thu Feb 15 02:43:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1i_32942/02_2024/7x1i_32942_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1i_32942/02_2024/7x1i_32942.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1i_32942/02_2024/7x1i_32942_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1i_32942/02_2024/7x1i_32942_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1i_32942/02_2024/7x1i_32942_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1i_32942/02_2024/7x1i_32942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1i_32942/02_2024/7x1i_32942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1i_32942/02_2024/7x1i_32942_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1i_32942/02_2024/7x1i_32942_neut_updated.pdb" } resolution = 2.94 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= 0.026 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 6 5.49 5 S 62 5.16 5 C 7176 2.51 5 N 1782 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10920 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5409 Classifications: {'peptide': 678} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 648} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5409 Classifications: {'peptide': 678} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 648} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PT5': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PT5:plan-1': 1, 'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PT5': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PT5:plan-1': 1, 'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 6.15, per 1000 atoms: 0.56 Number of scatterers: 10920 At special positions: 0 Unit cell: (84.563, 125.613, 109.193, 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 62 16.00 P 6 15.00 O 1894 8.00 N 1782 7.00 C 7176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.74 Conformation dependent library (CDL) restraints added in 2.1 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 4 sheets defined 61.5% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.13 Creating SS restraints... Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.513A pdb=" N MET A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 276 removed outlier: 3.541A pdb=" N MET A 275 " --> pdb=" O THR A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.969A pdb=" N PHE A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 361' Processing helix chain 'A' and resid 372 through 400 removed outlier: 3.609A pdb=" N LEU A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) Proline residue: A 389 - end of helix Processing helix chain 'A' and resid 407 through 424 Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 456 through 476 Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 488 through 516 removed outlier: 4.543A pdb=" N ILE A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 596 removed outlier: 4.121A pdb=" N LYS A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LYS A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 612 through 625 Processing helix chain 'A' and resid 650 through 652 No H-bonds generated for 'chain 'A' and resid 650 through 652' Processing helix chain 'A' and resid 658 through 683 Processing helix chain 'A' and resid 696 through 712 removed outlier: 3.719A pdb=" N GLY A 709 " --> pdb=" O ILE A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 732 Proline residue: A 726 - end of helix Processing helix chain 'A' and resid 756 through 769 removed outlier: 4.004A pdb=" N LEU A 769 " --> pdb=" O VAL A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 778 removed outlier: 3.884A pdb=" N LEU A 776 " --> pdb=" O LEU A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 796 removed outlier: 3.622A pdb=" N LEU A 796 " --> pdb=" O ALA A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 808 Processing helix chain 'A' and resid 812 through 814 No H-bonds generated for 'chain 'A' and resid 812 through 814' Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 826 through 847 Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 858 through 870 removed outlier: 4.199A pdb=" N ILE A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) Proline residue: A 867 - end of helix Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.647A pdb=" N ILE A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 872 through 876' Processing helix chain 'A' and resid 879 through 886 removed outlier: 3.501A pdb=" N MET A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 135 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 173 through 179 removed outlier: 3.513A pdb=" N MET B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 276 removed outlier: 3.541A pdb=" N MET B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 291 through 306 Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.969A pdb=" N PHE B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 361' Processing helix chain 'B' and resid 372 through 400 removed outlier: 3.609A pdb=" N LEU B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) Proline residue: B 389 - end of helix Processing helix chain 'B' and resid 407 through 424 Processing helix chain 'B' and resid 436 through 451 Processing helix chain 'B' and resid 456 through 476 Processing helix chain 'B' and resid 479 through 485 Processing helix chain 'B' and resid 488 through 516 removed outlier: 4.544A pdb=" N ILE B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 4.121A pdb=" N LYS B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS B 596 " --> pdb=" O TYR B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 612 through 625 Processing helix chain 'B' and resid 650 through 652 No H-bonds generated for 'chain 'B' and resid 650 through 652' Processing helix chain 'B' and resid 658 through 683 Processing helix chain 'B' and resid 696 through 712 removed outlier: 3.719A pdb=" N GLY B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 732 Proline residue: B 726 - end of helix Processing helix chain 'B' and resid 756 through 769 removed outlier: 4.004A pdb=" N LEU B 769 " --> pdb=" O VAL B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 778 removed outlier: 3.884A pdb=" N LEU B 776 " --> pdb=" O LEU B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 796 removed outlier: 3.622A pdb=" N LEU B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 808 Processing helix chain 'B' and resid 812 through 814 No H-bonds generated for 'chain 'B' and resid 812 through 814' Processing helix chain 'B' and resid 819 through 823 Processing helix chain 'B' and resid 826 through 847 Processing helix chain 'B' and resid 852 through 856 Processing helix chain 'B' and resid 858 through 870 removed outlier: 4.199A pdb=" N ILE B 866 " --> pdb=" O MET B 862 " (cutoff:3.500A) Proline residue: B 867 - end of helix Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.647A pdb=" N ILE B 876 " --> pdb=" O LEU B 872 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 872 through 876' Processing helix chain 'B' and resid 879 through 886 removed outlier: 3.500A pdb=" N MET B 885 " --> pdb=" O TYR B 881 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 196 through 198 removed outlier: 4.219A pdb=" N ASP A 196 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE A 249 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A 217 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 251 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N CYS A 219 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL A 253 " --> pdb=" O CYS A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 733 through 735 removed outlier: 3.962A pdb=" N ASN A 750 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 196 through 198 removed outlier: 4.219A pdb=" N ASP B 196 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE B 249 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE B 217 " --> pdb=" O PHE B 249 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE B 251 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N CYS B 219 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL B 253 " --> pdb=" O CYS B 219 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 733 through 735 removed outlier: 3.962A pdb=" N ASN B 750 " --> pdb=" O LEU B 734 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1638 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: 2.93 Time building geometry restraints manager: 4.91 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: 1737 1.32 - 1.45: 2917 1.45 - 1.57: 6400 1.57 - 1.69: 8 1.69 - 1.81: 102 Bond restraints: 11164 Sorted by residual: bond pdb=" C19 PT5 A2000 " pdb=" C20 PT5 A2000 " ideal model delta sigma weight residual 1.588 1.317 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C19 PT5 B2000 " pdb=" C20 PT5 B2000 " ideal model delta sigma weight residual 1.588 1.317 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C15 PT5 B2000 " pdb=" C16 PT5 B2000 " ideal model delta sigma weight residual 1.360 1.519 -0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" C15 PT5 A2000 " pdb=" C16 PT5 A2000 " ideal model delta sigma weight residual 1.360 1.519 -0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" C18 PT5 A2000 " pdb=" C19 PT5 A2000 " ideal model delta sigma weight residual 1.338 1.494 -0.156 2.00e-02 2.50e+03 6.08e+01 ... (remaining 11159 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.42: 392 107.42 - 114.29: 6635 114.29 - 121.17: 5607 121.17 - 128.04: 2408 128.04 - 134.91: 100 Bond angle restraints: 15142 Sorted by residual: angle pdb=" C18 PT5 A2000 " pdb=" C19 PT5 A2000 " pdb=" C20 PT5 A2000 " ideal model delta sigma weight residual 85.86 126.10 -40.24 3.00e+00 1.11e-01 1.80e+02 angle pdb=" C18 PT5 B2000 " pdb=" C19 PT5 B2000 " pdb=" C20 PT5 B2000 " ideal model delta sigma weight residual 85.86 126.07 -40.21 3.00e+00 1.11e-01 1.80e+02 angle pdb=" C15 PT5 B2000 " pdb=" C16 PT5 B2000 " pdb=" C17 PT5 B2000 " ideal model delta sigma weight residual 152.67 114.85 37.82 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C15 PT5 A2000 " pdb=" C16 PT5 A2000 " pdb=" C17 PT5 A2000 " ideal model delta sigma weight residual 152.67 114.85 37.82 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C19 PT5 B2000 " pdb=" C20 PT5 B2000 " pdb=" C21 PT5 B2000 " ideal model delta sigma weight residual 109.51 126.35 -16.84 3.00e+00 1.11e-01 3.15e+01 ... (remaining 15137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 6588 35.72 - 71.43: 46 71.43 - 107.15: 6 107.15 - 142.86: 2 142.86 - 178.58: 4 Dihedral angle restraints: 6646 sinusoidal: 2672 harmonic: 3974 Sorted by residual: dihedral pdb=" C12 PT5 B2000 " pdb=" C13 PT5 B2000 " pdb=" C14 PT5 B2000 " pdb=" C15 PT5 B2000 " ideal model delta sinusoidal sigma weight residual 21.27 -160.15 -178.58 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C12 PT5 A2000 " pdb=" C13 PT5 A2000 " pdb=" C14 PT5 A2000 " pdb=" C15 PT5 A2000 " ideal model delta sinusoidal sigma weight residual 21.27 -160.19 -178.54 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C32 PT5 A2000 " pdb=" C11 PT5 A2000 " pdb=" C31 PT5 A2000 " pdb=" O18 PT5 A2000 " ideal model delta sinusoidal sigma weight residual -171.11 -15.16 -155.95 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 6643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.001: 1782 1.001 - 2.001: 0 2.001 - 3.002: 0 3.002 - 4.003: 0 4.003 - 5.004: 2 Chirality restraints: 1784 Sorted by residual: chirality pdb=" C2 PT5 A2000 " pdb=" C1 PT5 A2000 " pdb=" C3 PT5 A2000 " pdb=" O2 PT5 A2000 " both_signs ideal model delta sigma weight residual False -2.52 2.49 -5.00 2.00e-01 2.50e+01 6.26e+02 chirality pdb=" C2 PT5 B2000 " pdb=" C1 PT5 B2000 " pdb=" C3 PT5 B2000 " pdb=" O2 PT5 B2000 " both_signs ideal model delta sigma weight residual False -2.52 2.48 -5.00 2.00e-01 2.50e+01 6.26e+02 chirality pdb=" CA ILE A 218 " pdb=" N ILE A 218 " pdb=" C ILE A 218 " pdb=" CB ILE A 218 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1781 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 PT5 A2000 " 0.138 2.00e-02 2.50e+03 2.50e-01 6.25e+02 pdb=" C15 PT5 A2000 " -0.325 2.00e-02 2.50e+03 pdb=" C16 PT5 A2000 " 0.326 2.00e-02 2.50e+03 pdb=" C17 PT5 A2000 " -0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 PT5 B2000 " -0.138 2.00e-02 2.50e+03 2.50e-01 6.25e+02 pdb=" C15 PT5 B2000 " 0.325 2.00e-02 2.50e+03 pdb=" C16 PT5 B2000 " -0.326 2.00e-02 2.50e+03 pdb=" C17 PT5 B2000 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 PT5 B2000 " 0.023 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C18 PT5 B2000 " -0.017 2.00e-02 2.50e+03 pdb=" C19 PT5 B2000 " -0.037 2.00e-02 2.50e+03 pdb=" C20 PT5 B2000 " 0.031 2.00e-02 2.50e+03 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1261 2.75 - 3.29: 11171 3.29 - 3.83: 18328 3.83 - 4.36: 22781 4.36 - 4.90: 39016 Nonbonded interactions: 92557 Sorted by model distance: nonbonded pdb=" O TYR A 421 " pdb=" OG SER A 425 " model vdw 2.217 2.440 nonbonded pdb=" O TYR B 421 " pdb=" OG SER B 425 " model vdw 2.217 2.440 nonbonded pdb=" O LEU B 600 " pdb=" NH1 ARG B 605 " model vdw 2.292 2.520 nonbonded pdb=" O LEU A 600 " pdb=" NH1 ARG A 605 " model vdw 2.293 2.520 nonbonded pdb=" O ILE B 498 " pdb=" OG1 THR B 501 " model vdw 2.296 2.440 ... (remaining 92552 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.420 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.300 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.006 0.271 11164 Z= 0.438 Angle : 0.873 40.245 15142 Z= 0.340 Chirality : 0.172 5.004 1784 Planarity : 0.009 0.250 1844 Dihedral : 11.342 178.576 4070 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.34 % Allowed : 2.21 % Favored : 97.45 % 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: 1.64 (0.23), residues: 1328 helix: 1.69 (0.18), residues: 858 sheet: 2.60 (0.62), residues: 66 loop : -0.45 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 717 HIS 0.002 0.000 HIS A 719 PHE 0.006 0.001 PHE A 393 TYR 0.005 0.001 TYR B 696 ARG 0.002 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 211 time to evaluate : 1.359 Fit side-chains REVERT: A 129 ASP cc_start: 0.7201 (m-30) cc_final: 0.7000 (m-30) REVERT: A 488 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.7896 (ttp80) REVERT: A 606 GLU cc_start: 0.7350 (tt0) cc_final: 0.7102 (tt0) REVERT: B 129 ASP cc_start: 0.7183 (m-30) cc_final: 0.6966 (m-30) REVERT: B 209 ARG cc_start: 0.6935 (ttp80) cc_final: 0.6662 (ttp80) REVERT: B 488 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.7870 (ttp80) REVERT: B 606 GLU cc_start: 0.7381 (tt0) cc_final: 0.7133 (tt0) outliers start: 4 outliers final: 0 residues processed: 215 average time/residue: 1.3270 time to fit residues: 305.1609 Evaluate side-chains 143 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 192 HIS A 199 GLN A 427 GLN A 593 GLN A 777 GLN A 830 HIS B 192 HIS B 199 GLN B 427 GLN B 593 GLN B 777 GLN B 830 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11164 Z= 0.252 Angle : 0.533 6.780 15142 Z= 0.264 Chirality : 0.041 0.148 1784 Planarity : 0.005 0.071 1844 Dihedral : 12.113 162.983 1520 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.72 % Allowed : 8.32 % Favored : 88.96 % 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: 1.66 (0.23), residues: 1328 helix: 1.68 (0.17), residues: 866 sheet: 3.05 (0.62), residues: 64 loop : -0.49 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 462 HIS 0.003 0.001 HIS B 819 PHE 0.016 0.002 PHE A 620 TYR 0.013 0.001 TYR B 722 ARG 0.005 0.000 ARG A 875 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 1.341 Fit side-chains REVERT: A 209 ARG cc_start: 0.6919 (ttp80) cc_final: 0.6625 (ptt90) REVERT: A 279 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7866 (mp) REVERT: A 606 GLU cc_start: 0.7379 (tt0) cc_final: 0.7145 (tt0) REVERT: A 793 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7698 (mp) REVERT: B 606 GLU cc_start: 0.7397 (tt0) cc_final: 0.7145 (tt0) REVERT: B 793 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7749 (mp) REVERT: B 854 MET cc_start: 0.7722 (ptm) cc_final: 0.7516 (ptm) outliers start: 32 outliers final: 17 residues processed: 170 average time/residue: 1.4359 time to fit residues: 260.4451 Evaluate side-chains 157 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS A 283 GLN A 427 GLN A 593 GLN A 777 GLN B 142 ASN B 192 HIS B 427 GLN B 777 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11164 Z= 0.328 Angle : 0.543 6.560 15142 Z= 0.272 Chirality : 0.042 0.153 1784 Planarity : 0.005 0.073 1844 Dihedral : 12.065 158.457 1520 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.80 % Allowed : 8.91 % Favored : 88.29 % 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: 1.39 (0.22), residues: 1328 helix: 1.55 (0.17), residues: 844 sheet: 3.12 (0.62), residues: 64 loop : -0.69 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 462 HIS 0.003 0.001 HIS B 601 PHE 0.018 0.002 PHE B 620 TYR 0.014 0.001 TYR A 722 ARG 0.006 0.001 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 1.092 Fit side-chains REVERT: A 209 ARG cc_start: 0.6919 (ttp80) cc_final: 0.6609 (ptt90) REVERT: A 304 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8449 (tp) REVERT: A 606 GLU cc_start: 0.7482 (tt0) cc_final: 0.7261 (tt0) REVERT: A 793 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7727 (mp) REVERT: B 304 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8439 (tp) REVERT: B 606 GLU cc_start: 0.7459 (tt0) cc_final: 0.7211 (tt0) REVERT: B 793 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7724 (mp) outliers start: 33 outliers final: 19 residues processed: 165 average time/residue: 1.3571 time to fit residues: 239.0162 Evaluate side-chains 155 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 777 GLN Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS A 199 GLN A 283 GLN B 192 HIS B 199 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11164 Z= 0.167 Angle : 0.466 5.544 15142 Z= 0.239 Chirality : 0.039 0.142 1784 Planarity : 0.005 0.074 1844 Dihedral : 11.463 147.776 1520 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.06 % Allowed : 9.34 % Favored : 87.61 % 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: 1.57 (0.22), residues: 1328 helix: 1.77 (0.17), residues: 846 sheet: 3.09 (0.62), residues: 64 loop : -0.82 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 778 HIS 0.003 0.001 HIS A 719 PHE 0.019 0.001 PHE A 620 TYR 0.013 0.001 TYR A 722 ARG 0.005 0.000 ARG A 875 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 0.867 Fit side-chains REVERT: A 209 ARG cc_start: 0.6879 (ttp80) cc_final: 0.6578 (ptt90) REVERT: A 304 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8451 (tp) REVERT: A 606 GLU cc_start: 0.7435 (tt0) cc_final: 0.7195 (tt0) REVERT: B 304 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8427 (tp) REVERT: B 606 GLU cc_start: 0.7472 (tt0) cc_final: 0.7239 (tt0) outliers start: 36 outliers final: 17 residues processed: 167 average time/residue: 1.2430 time to fit residues: 221.4939 Evaluate side-chains 153 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 0.0470 chunk 116 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS A 283 GLN B 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11164 Z= 0.186 Angle : 0.474 6.442 15142 Z= 0.240 Chirality : 0.039 0.145 1784 Planarity : 0.005 0.073 1844 Dihedral : 10.745 132.148 1520 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.38 % Allowed : 11.04 % Favored : 86.59 % 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: 1.64 (0.23), residues: 1328 helix: 1.79 (0.17), residues: 858 sheet: 3.18 (0.62), residues: 64 loop : -0.79 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 462 HIS 0.003 0.001 HIS B 719 PHE 0.018 0.001 PHE B 620 TYR 0.013 0.001 TYR A 722 ARG 0.007 0.000 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 0.914 Fit side-chains REVERT: A 209 ARG cc_start: 0.6894 (ttp80) cc_final: 0.6622 (ttp80) REVERT: A 304 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8453 (tp) REVERT: A 606 GLU cc_start: 0.7444 (tt0) cc_final: 0.7208 (tt0) REVERT: B 158 ARG cc_start: 0.7454 (ttm170) cc_final: 0.7220 (ttm170) REVERT: B 304 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8432 (tp) REVERT: B 606 GLU cc_start: 0.7453 (tt0) cc_final: 0.7222 (tt0) outliers start: 28 outliers final: 22 residues processed: 155 average time/residue: 1.0290 time to fit residues: 170.1305 Evaluate side-chains 158 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS B 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11164 Z= 0.298 Angle : 0.519 5.830 15142 Z= 0.262 Chirality : 0.041 0.151 1784 Planarity : 0.005 0.072 1844 Dihedral : 10.344 124.824 1520 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.80 % Allowed : 11.21 % Favored : 85.99 % 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: 1.46 (0.22), residues: 1328 helix: 1.67 (0.17), residues: 844 sheet: 3.18 (0.61), residues: 64 loop : -0.84 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 462 HIS 0.003 0.001 HIS B 719 PHE 0.019 0.002 PHE A 620 TYR 0.014 0.001 TYR B 722 ARG 0.002 0.000 ARG A 875 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.316 Fit side-chains REVERT: A 209 ARG cc_start: 0.6899 (ttp80) cc_final: 0.6649 (ttp80) REVERT: A 304 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8471 (tp) REVERT: A 606 GLU cc_start: 0.7444 (tt0) cc_final: 0.7218 (tt0) REVERT: B 158 ARG cc_start: 0.7473 (ttm170) cc_final: 0.7227 (ttm170) REVERT: B 304 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8482 (tp) REVERT: B 606 GLU cc_start: 0.7495 (tt0) cc_final: 0.7245 (tt0) outliers start: 33 outliers final: 23 residues processed: 157 average time/residue: 1.0464 time to fit residues: 175.7932 Evaluate side-chains 162 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS B 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11164 Z= 0.340 Angle : 0.546 5.874 15142 Z= 0.277 Chirality : 0.042 0.157 1784 Planarity : 0.005 0.073 1844 Dihedral : 10.000 125.549 1520 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.72 % Allowed : 11.54 % Favored : 85.74 % 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: 1.24 (0.22), residues: 1328 helix: 1.49 (0.17), residues: 844 sheet: 3.16 (0.61), residues: 64 loop : -0.92 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 462 HIS 0.003 0.001 HIS A 719 PHE 0.019 0.002 PHE A 620 TYR 0.015 0.001 TYR A 722 ARG 0.006 0.000 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.611 Fit side-chains REVERT: A 209 ARG cc_start: 0.6910 (ttp80) cc_final: 0.6647 (ptt90) REVERT: A 304 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8475 (tp) REVERT: A 793 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7861 (mp) REVERT: B 158 ARG cc_start: 0.7465 (ttm170) cc_final: 0.7203 (ttm170) REVERT: B 304 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8476 (tp) REVERT: B 793 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7855 (mp) outliers start: 32 outliers final: 19 residues processed: 151 average time/residue: 1.3563 time to fit residues: 219.8795 Evaluate side-chains 154 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS B 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11164 Z= 0.184 Angle : 0.465 5.496 15142 Z= 0.239 Chirality : 0.038 0.144 1784 Planarity : 0.005 0.072 1844 Dihedral : 9.505 118.009 1520 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.38 % Allowed : 11.80 % Favored : 85.82 % 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: 1.51 (0.23), residues: 1328 helix: 1.74 (0.17), residues: 846 sheet: 3.16 (0.62), residues: 64 loop : -0.90 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 462 HIS 0.004 0.001 HIS A 719 PHE 0.018 0.001 PHE A 620 TYR 0.014 0.001 TYR B 722 ARG 0.004 0.000 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.257 Fit side-chains REVERT: A 209 ARG cc_start: 0.6925 (ttp80) cc_final: 0.6662 (ptt90) REVERT: A 304 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8456 (tp) REVERT: A 793 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7746 (mp) REVERT: B 304 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8455 (tp) REVERT: B 793 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7731 (mp) outliers start: 28 outliers final: 17 residues processed: 156 average time/residue: 1.3594 time to fit residues: 227.3911 Evaluate side-chains 152 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 0.0040 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS B 192 HIS B 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11164 Z= 0.254 Angle : 0.519 7.676 15142 Z= 0.262 Chirality : 0.040 0.146 1784 Planarity : 0.005 0.072 1844 Dihedral : 9.489 118.153 1520 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.63 % Allowed : 12.14 % Favored : 85.23 % 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: 1.40 (0.23), residues: 1328 helix: 1.64 (0.17), residues: 846 sheet: 3.20 (0.62), residues: 64 loop : -0.91 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 462 HIS 0.003 0.001 HIS B 719 PHE 0.019 0.001 PHE A 620 TYR 0.014 0.001 TYR A 722 ARG 0.004 0.000 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 1.280 Fit side-chains REVERT: A 209 ARG cc_start: 0.6895 (ttp80) cc_final: 0.6632 (ptt90) REVERT: A 304 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8455 (tp) REVERT: A 793 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7819 (mp) REVERT: B 304 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8456 (tp) REVERT: B 793 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7811 (mp) outliers start: 31 outliers final: 21 residues processed: 150 average time/residue: 1.4514 time to fit residues: 232.8284 Evaluate side-chains 158 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 0.0060 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS B 192 HIS B 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11164 Z= 0.211 Angle : 0.502 7.344 15142 Z= 0.254 Chirality : 0.039 0.145 1784 Planarity : 0.005 0.072 1844 Dihedral : 9.373 115.673 1520 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.21 % Allowed : 12.56 % Favored : 85.23 % 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: 1.46 (0.23), residues: 1328 helix: 1.68 (0.17), residues: 846 sheet: 3.21 (0.62), residues: 64 loop : -0.87 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 462 HIS 0.003 0.001 HIS B 719 PHE 0.018 0.001 PHE A 620 TYR 0.014 0.001 TYR A 722 ARG 0.004 0.000 ARG B 875 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.257 Fit side-chains REVERT: A 209 ARG cc_start: 0.6925 (ttp80) cc_final: 0.6664 (ptt90) REVERT: A 296 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7363 (mt-10) REVERT: A 304 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8453 (tp) REVERT: A 793 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7826 (mp) REVERT: B 304 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8449 (tp) REVERT: B 793 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7815 (mp) outliers start: 26 outliers final: 22 residues processed: 151 average time/residue: 1.4389 time to fit residues: 232.3343 Evaluate side-chains 163 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 809 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS B 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.100297 restraints weight = 12541.824| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.81 r_work: 0.2969 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.215 11164 Z= 0.341 Angle : 0.802 59.146 15142 Z= 0.465 Chirality : 0.047 1.015 1784 Planarity : 0.005 0.072 1844 Dihedral : 9.380 115.717 1520 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.04 % Allowed : 12.82 % Favored : 85.14 % Cbeta Deviations : 0.08 % 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: 1.40 (0.23), residues: 1328 helix: 1.62 (0.17), residues: 846 sheet: 3.21 (0.62), residues: 64 loop : -0.88 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 462 HIS 0.004 0.001 HIS B 719 PHE 0.018 0.001 PHE A 620 TYR 0.014 0.001 TYR A 722 ARG 0.004 0.000 ARG B 875 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3987.36 seconds wall clock time: 97 minutes 38.25 seconds (5858.25 seconds total)