Starting phenix.real_space_refine on Thu Feb 15 11:45:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpb_4612/02_2024/6qpb_4612_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpb_4612/02_2024/6qpb_4612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpb_4612/02_2024/6qpb_4612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpb_4612/02_2024/6qpb_4612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpb_4612/02_2024/6qpb_4612_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpb_4612/02_2024/6qpb_4612_updated.pdb" } resolution = 3.6 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= 0.002 sd= 0.014 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 80 5.16 5 C 8000 2.51 5 N 1938 2.21 5 O 2134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 51": "OE1" <-> "OE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A ARG 810": "NH1" <-> "NH2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "B ARG 810": "NH1" <-> "NH2" Residue "B GLU 871": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12154 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 6039 Classifications: {'peptide': 731} Link IDs: {'PTRANS': 34, 'TRANS': 696} Chain breaks: 6 Chain: "B" Number of atoms: 6039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 6039 Classifications: {'peptide': 731} Link IDs: {'PTRANS': 34, 'TRANS': 696} Chain breaks: 6 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.92, per 1000 atoms: 0.57 Number of scatterers: 12154 At special positions: 0 Unit cell: (88.044, 114.356, 116.38, 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 80 16.00 P 2 15.00 O 2134 8.00 N 1938 7.00 C 8000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.04 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.04 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.04 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.18 Conformation dependent library (CDL) restraints added in 2.2 seconds 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 56.6% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 91 through 108 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 206 through 219 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 265 through 272 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 285 through 326 removed outlier: 7.497A pdb=" N GLU A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N LYS A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 365 through 374 removed outlier: 4.711A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 407 removed outlier: 3.813A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 448 through 488 Processing helix chain 'A' and resid 505 through 538 Processing helix chain 'A' and resid 544 through 572 removed outlier: 5.111A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 623 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 686 through 708 Proline residue: A 689 - end of helix removed outlier: 3.506A pdb=" N LEU A 698 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 700 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP A 705 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 708 " --> pdb=" O TRP A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 4.007A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 759 Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 826 through 856 Processing helix chain 'A' and resid 862 through 876 Processing helix chain 'B' and resid 91 through 108 Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 206 through 219 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 285 through 326 removed outlier: 7.496A pdb=" N GLU B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N LYS B 295 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 296 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 365 through 374 removed outlier: 4.712A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 407 removed outlier: 3.812A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 426 Processing helix chain 'B' and resid 448 through 488 Processing helix chain 'B' and resid 505 through 538 Processing helix chain 'B' and resid 544 through 572 removed outlier: 5.111A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 623 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 649 through 654 Processing helix chain 'B' and resid 665 through 679 Processing helix chain 'B' and resid 686 through 708 Proline residue: B 689 - end of helix removed outlier: 3.507A pdb=" N LEU B 698 " --> pdb=" O ASN B 695 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 700 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP B 705 " --> pdb=" O VAL B 702 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR B 708 " --> pdb=" O TRP B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 4.006A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 759 Processing helix chain 'B' and resid 776 through 780 Processing helix chain 'B' and resid 826 through 856 Processing helix chain 'B' and resid 862 through 876 Processing sheet with id= A, first strand: chain 'A' and resid 244 through 247 removed outlier: 4.058A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 782 through 785 Processing sheet with id= C, first strand: chain 'B' and resid 244 through 247 removed outlier: 4.058A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 782 through 785 642 hydrogen bonds defined for protein. 1830 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.63 Time building geometry restraints manager: 5.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2150 1.33 - 1.46: 4100 1.46 - 1.59: 6114 1.59 - 1.72: 2 1.72 - 1.85: 122 Bond restraints: 12488 Sorted by residual: bond pdb=" O3 P1O B1001 " pdb=" P1 P1O B1001 " ideal model delta sigma weight residual 1.648 1.777 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" O3 P1O A1001 " pdb=" P1 P1O A1001 " ideal model delta sigma weight residual 1.648 1.776 -0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C19 P1O A1001 " pdb=" C20 P1O A1001 " ideal model delta sigma weight residual 1.502 1.579 -0.077 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C19 P1O B1001 " pdb=" C20 P1O B1001 " ideal model delta sigma weight residual 1.502 1.578 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C7 P1O B1001 " pdb=" C8 P1O B1001 " ideal model delta sigma weight residual 1.515 1.588 -0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 12483 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.86: 374 106.86 - 114.08: 6877 114.08 - 121.31: 6949 121.31 - 128.53: 2618 128.53 - 135.75: 110 Bond angle restraints: 16928 Sorted by residual: angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 117.03 -6.33 1.22e+00 6.72e-01 2.69e+01 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 116.99 -6.29 1.22e+00 6.72e-01 2.66e+01 angle pdb=" C GLY A 589 " pdb=" N LYS A 590 " pdb=" CA LYS A 590 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLY B 589 " pdb=" N LYS B 590 " pdb=" CA LYS B 590 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C TRP A 408 " pdb=" N ASP A 409 " pdb=" CA ASP A 409 " ideal model delta sigma weight residual 122.46 128.69 -6.23 1.41e+00 5.03e-01 1.95e+01 ... (remaining 16923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 6848 22.60 - 45.21: 468 45.21 - 67.81: 50 67.81 - 90.41: 12 90.41 - 113.02: 2 Dihedral angle restraints: 7380 sinusoidal: 3048 harmonic: 4332 Sorted by residual: dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual 93.00 3.54 89.46 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS B 338 " pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " pdb=" CB CYS B 365 " ideal model delta sinusoidal sigma weight residual 93.00 3.56 89.44 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 154.79 -61.79 1 1.00e+01 1.00e-02 5.06e+01 ... (remaining 7377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.009: 1832 1.009 - 2.018: 0 2.018 - 3.026: 0 3.026 - 4.035: 0 4.035 - 5.044: 2 Chirality restraints: 1834 Sorted by residual: chirality pdb=" C7 P1O B1001 " pdb=" C6 P1O B1001 " pdb=" C8 P1O B1001 " pdb=" O7 P1O B1001 " both_signs ideal model delta sigma weight residual False -2.35 2.69 -5.04 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" C7 P1O A1001 " pdb=" C6 P1O A1001 " pdb=" C8 P1O A1001 " pdb=" O7 P1O A1001 " both_signs ideal model delta sigma weight residual False -2.35 2.69 -5.04 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 1831 not shown) Planarity restraints: 2100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 763 " 0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO A 764 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 764 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 764 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 763 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO B 764 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 762 " 0.052 5.00e-02 4.00e+02 7.71e-02 9.51e+00 pdb=" N PRO B 763 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 763 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 763 " 0.041 5.00e-02 4.00e+02 ... (remaining 2097 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 146 2.65 - 3.21: 10626 3.21 - 3.77: 19435 3.77 - 4.34: 25692 4.34 - 4.90: 42333 Nonbonded interactions: 98232 Sorted by model distance: nonbonded pdb=" O THR A 364 " pdb=" OG SER A 367 " model vdw 2.084 2.440 nonbonded pdb=" O THR B 364 " pdb=" OG SER B 367 " model vdw 2.085 2.440 nonbonded pdb=" O ASP A 46 " pdb=" OG SER A 103 " model vdw 2.275 2.440 nonbonded pdb=" O ASP B 46 " pdb=" OG SER B 103 " model vdw 2.276 2.440 nonbonded pdb=" O ILE A 744 " pdb=" OG SER A 748 " model vdw 2.339 2.440 ... (remaining 98227 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 group one per residue 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: 0.520 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: 3.020 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 35.570 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 0.129 12488 Z= 0.366 Angle : 0.876 10.753 16928 Z= 0.487 Chirality : 0.174 5.044 1834 Planarity : 0.009 0.085 2100 Dihedral : 14.703 113.018 4574 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % 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: -2.86 (0.17), residues: 1434 helix: -1.45 (0.13), residues: 854 sheet: -1.18 (0.55), residues: 64 loop : -2.58 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 619 HIS 0.007 0.001 HIS B 830 PHE 0.028 0.002 PHE B 73 TYR 0.020 0.002 TYR A 222 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.523 Fit side-chains REVERT: A 381 ILE cc_start: 0.8655 (mt) cc_final: 0.8301 (mm) REVERT: A 384 VAL cc_start: 0.9064 (t) cc_final: 0.8829 (m) REVERT: A 522 MET cc_start: 0.7545 (mmm) cc_final: 0.7083 (mmm) REVERT: A 811 ASP cc_start: 0.7920 (t0) cc_final: 0.7532 (m-30) REVERT: A 851 PHE cc_start: 0.7787 (m-80) cc_final: 0.7506 (m-10) REVERT: B 60 ASP cc_start: 0.7902 (p0) cc_final: 0.7643 (p0) REVERT: B 381 ILE cc_start: 0.8629 (mt) cc_final: 0.8300 (mm) REVERT: B 384 VAL cc_start: 0.9107 (t) cc_final: 0.8880 (m) REVERT: B 522 MET cc_start: 0.7531 (mmm) cc_final: 0.7252 (mmm) REVERT: B 706 LYS cc_start: 0.8924 (mttt) cc_final: 0.8702 (mtmt) REVERT: B 810 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.7605 (ttt90) REVERT: B 811 ASP cc_start: 0.7862 (t0) cc_final: 0.7492 (m-30) REVERT: B 851 PHE cc_start: 0.7863 (m-80) cc_final: 0.7535 (m-10) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2550 time to fit residues: 75.7458 Evaluate side-chains 136 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN A 623 GLN A 696 ASN A 796 ASN B 401 GLN B 418 GLN B 623 GLN B 696 ASN B 796 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12488 Z= 0.158 Angle : 0.528 7.982 16928 Z= 0.279 Chirality : 0.040 0.150 1834 Planarity : 0.006 0.073 2100 Dihedral : 8.306 143.684 1676 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.12 % Allowed : 10.39 % Favored : 87.48 % 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: -0.63 (0.20), residues: 1434 helix: 0.39 (0.16), residues: 882 sheet: -0.65 (0.59), residues: 64 loop : -1.82 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 619 HIS 0.004 0.001 HIS A 830 PHE 0.018 0.001 PHE B 558 TYR 0.019 0.001 TYR B 855 ARG 0.002 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 1.379 Fit side-chains REVERT: A 524 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8710 (mp) REVERT: A 810 ARG cc_start: 0.8016 (ttt180) cc_final: 0.7804 (tmm-80) REVERT: A 811 ASP cc_start: 0.8064 (t0) cc_final: 0.7446 (m-30) REVERT: A 851 PHE cc_start: 0.7652 (m-80) cc_final: 0.7358 (m-10) REVERT: B 108 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7228 (t-90) REVERT: B 354 ARG cc_start: 0.7167 (ttt180) cc_final: 0.6913 (tpt-90) REVERT: B 522 MET cc_start: 0.7111 (mmm) cc_final: 0.6867 (mmm) REVERT: B 524 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8712 (mp) REVERT: B 810 ARG cc_start: 0.7986 (ttt180) cc_final: 0.7771 (tmm-80) REVERT: B 811 ASP cc_start: 0.8002 (t0) cc_final: 0.7392 (m-30) REVERT: B 842 MET cc_start: 0.7852 (ttp) cc_final: 0.7648 (ttp) REVERT: B 851 PHE cc_start: 0.7739 (m-80) cc_final: 0.7426 (m-10) outliers start: 28 outliers final: 14 residues processed: 183 average time/residue: 0.2105 time to fit residues: 57.6710 Evaluate side-chains 164 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN A 696 ASN B 674 GLN B 696 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12488 Z= 0.301 Angle : 0.568 6.807 16928 Z= 0.299 Chirality : 0.042 0.166 1834 Planarity : 0.006 0.069 2100 Dihedral : 8.062 134.580 1676 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.11 % Allowed : 12.29 % Favored : 84.60 % 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: -0.05 (0.21), residues: 1434 helix: 0.85 (0.16), residues: 872 sheet: -0.68 (0.63), residues: 62 loop : -1.49 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 619 HIS 0.007 0.001 HIS B 830 PHE 0.017 0.002 PHE A 73 TYR 0.017 0.002 TYR B 580 ARG 0.002 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 146 time to evaluate : 1.499 Fit side-chains REVERT: A 108 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7435 (t-90) REVERT: A 277 ARG cc_start: 0.7173 (mtt180) cc_final: 0.6699 (mmp-170) REVERT: A 773 MET cc_start: 0.9336 (mmm) cc_final: 0.9131 (tpp) REVERT: A 851 PHE cc_start: 0.7762 (m-80) cc_final: 0.7529 (m-10) REVERT: B 108 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7420 (t-90) REVERT: B 277 ARG cc_start: 0.7153 (mtt180) cc_final: 0.6714 (mmp-170) REVERT: B 522 MET cc_start: 0.7279 (mmm) cc_final: 0.6999 (mmm) REVERT: B 773 MET cc_start: 0.9342 (mmm) cc_final: 0.8935 (tpp) REVERT: B 851 PHE cc_start: 0.7801 (m-80) cc_final: 0.7542 (m-10) outliers start: 41 outliers final: 27 residues processed: 177 average time/residue: 0.2363 time to fit residues: 61.9213 Evaluate side-chains 149 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 0.0170 chunk 133 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 696 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12488 Z= 0.141 Angle : 0.493 6.917 16928 Z= 0.256 Chirality : 0.039 0.142 1834 Planarity : 0.005 0.069 2100 Dihedral : 7.691 130.799 1676 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.66 % Allowed : 13.88 % Favored : 83.46 % 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: 0.55 (0.22), residues: 1434 helix: 1.30 (0.17), residues: 882 sheet: -0.34 (0.62), residues: 64 loop : -1.27 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 397 HIS 0.002 0.000 HIS B 830 PHE 0.020 0.001 PHE B 789 TYR 0.021 0.001 TYR B 855 ARG 0.002 0.000 ARG A 810 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 1.598 Fit side-chains REVERT: A 108 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7541 (t-90) REVERT: A 138 TYR cc_start: 0.7987 (m-80) cc_final: 0.7111 (m-80) REVERT: A 277 ARG cc_start: 0.7004 (mtt180) cc_final: 0.6566 (mmp-170) REVERT: A 773 MET cc_start: 0.9395 (mmm) cc_final: 0.9173 (tpp) REVERT: A 811 ASP cc_start: 0.7857 (t0) cc_final: 0.7218 (m-30) REVERT: A 842 MET cc_start: 0.8183 (ttt) cc_final: 0.7842 (ttp) REVERT: A 851 PHE cc_start: 0.7650 (m-80) cc_final: 0.7355 (m-10) REVERT: B 108 HIS cc_start: 0.8354 (OUTLIER) cc_final: 0.7584 (t-90) REVERT: B 138 TYR cc_start: 0.7981 (m-80) cc_final: 0.7091 (m-80) REVERT: B 277 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6603 (mmp-170) REVERT: B 522 MET cc_start: 0.7108 (mmm) cc_final: 0.6765 (mmm) REVERT: B 553 MET cc_start: 0.8200 (tpp) cc_final: 0.7854 (tpp) REVERT: B 604 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8181 (tm-30) REVERT: B 773 MET cc_start: 0.9402 (mmm) cc_final: 0.9164 (tpp) REVERT: B 811 ASP cc_start: 0.7855 (t0) cc_final: 0.7170 (m-30) REVERT: B 851 PHE cc_start: 0.7711 (m-80) cc_final: 0.7406 (m-10) outliers start: 35 outliers final: 17 residues processed: 165 average time/residue: 0.2093 time to fit residues: 52.8629 Evaluate side-chains 152 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 58 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 126 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN B 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12488 Z= 0.143 Angle : 0.511 9.335 16928 Z= 0.260 Chirality : 0.039 0.149 1834 Planarity : 0.005 0.068 2100 Dihedral : 7.595 129.902 1676 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.50 % Allowed : 15.02 % Favored : 82.47 % 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: 0.93 (0.22), residues: 1434 helix: 1.58 (0.17), residues: 878 sheet: -0.07 (0.64), residues: 64 loop : -1.04 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 397 HIS 0.003 0.000 HIS B 830 PHE 0.019 0.001 PHE B 231 TYR 0.018 0.001 TYR B 855 ARG 0.001 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 1.379 Fit side-chains REVERT: A 47 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6700 (t80) REVERT: A 108 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.7524 (t-90) REVERT: A 138 TYR cc_start: 0.7995 (m-80) cc_final: 0.7187 (m-80) REVERT: A 277 ARG cc_start: 0.6951 (mtt180) cc_final: 0.6538 (mmp-170) REVERT: A 348 MET cc_start: 0.8783 (mmm) cc_final: 0.8577 (mmm) REVERT: A 555 MET cc_start: 0.8397 (tpt) cc_final: 0.8125 (mmt) REVERT: A 773 MET cc_start: 0.9395 (mmm) cc_final: 0.8798 (tpp) REVERT: A 811 ASP cc_start: 0.7848 (t0) cc_final: 0.7169 (m-30) REVERT: A 842 MET cc_start: 0.8155 (ttt) cc_final: 0.7798 (ttp) REVERT: A 851 PHE cc_start: 0.7625 (m-80) cc_final: 0.7378 (m-10) REVERT: B 47 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6535 (t80) REVERT: B 108 HIS cc_start: 0.8324 (OUTLIER) cc_final: 0.7559 (t-90) REVERT: B 138 TYR cc_start: 0.8027 (m-80) cc_final: 0.7238 (m-80) REVERT: B 277 ARG cc_start: 0.6956 (mtt180) cc_final: 0.6563 (mmp-170) REVERT: B 522 MET cc_start: 0.7105 (mmm) cc_final: 0.6781 (mmm) REVERT: B 555 MET cc_start: 0.8450 (tpt) cc_final: 0.8097 (mmt) REVERT: B 668 TYR cc_start: 0.8891 (m-80) cc_final: 0.8686 (m-80) REVERT: B 773 MET cc_start: 0.9397 (mmm) cc_final: 0.9154 (tpp) REVERT: B 851 PHE cc_start: 0.7634 (m-80) cc_final: 0.7370 (m-10) outliers start: 33 outliers final: 18 residues processed: 172 average time/residue: 0.2011 time to fit residues: 52.9611 Evaluate side-chains 157 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.2980 chunk 127 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 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 674 GLN A 696 ASN B 696 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12488 Z= 0.191 Angle : 0.522 8.666 16928 Z= 0.269 Chirality : 0.040 0.143 1834 Planarity : 0.005 0.067 2100 Dihedral : 7.619 129.443 1676 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.72 % Allowed : 15.33 % Favored : 80.96 % 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: 1.02 (0.22), residues: 1434 helix: 1.64 (0.17), residues: 878 sheet: -0.16 (0.64), residues: 64 loop : -0.96 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 397 HIS 0.004 0.001 HIS B 830 PHE 0.014 0.001 PHE A 558 TYR 0.017 0.001 TYR B 855 ARG 0.001 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 139 time to evaluate : 1.496 Fit side-chains REVERT: A 47 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6943 (t80) REVERT: A 93 LYS cc_start: 0.7847 (tppt) cc_final: 0.7616 (mtmt) REVERT: A 108 HIS cc_start: 0.8339 (OUTLIER) cc_final: 0.7552 (t-90) REVERT: A 138 TYR cc_start: 0.8058 (m-80) cc_final: 0.7288 (m-80) REVERT: A 277 ARG cc_start: 0.7110 (mtt180) cc_final: 0.6638 (mmp-170) REVERT: A 348 MET cc_start: 0.8762 (mmm) cc_final: 0.8517 (mmm) REVERT: A 773 MET cc_start: 0.9322 (mmm) cc_final: 0.8753 (tpp) REVERT: A 842 MET cc_start: 0.8203 (ttt) cc_final: 0.7861 (ttp) REVERT: A 851 PHE cc_start: 0.7663 (m-80) cc_final: 0.7407 (m-10) REVERT: B 47 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6834 (t80) REVERT: B 108 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7553 (t-90) REVERT: B 138 TYR cc_start: 0.8052 (m-80) cc_final: 0.7287 (m-80) REVERT: B 277 ARG cc_start: 0.7061 (mtt180) cc_final: 0.6644 (mmp-170) REVERT: B 522 MET cc_start: 0.7154 (mmm) cc_final: 0.6845 (mmm) REVERT: B 557 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8277 (mp) REVERT: B 773 MET cc_start: 0.9324 (mmm) cc_final: 0.8741 (tpp) REVERT: B 851 PHE cc_start: 0.7738 (m-80) cc_final: 0.7501 (m-10) outliers start: 49 outliers final: 29 residues processed: 178 average time/residue: 0.2098 time to fit residues: 57.1612 Evaluate side-chains 169 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 118 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 85 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN B 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12488 Z= 0.156 Angle : 0.501 9.621 16928 Z= 0.256 Chirality : 0.039 0.144 1834 Planarity : 0.005 0.067 2100 Dihedral : 7.629 128.965 1676 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.73 % Allowed : 16.69 % Favored : 80.58 % 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 (0.22), residues: 1434 helix: 1.78 (0.17), residues: 878 sheet: -0.17 (0.64), residues: 64 loop : -0.91 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 397 HIS 0.003 0.001 HIS B 830 PHE 0.021 0.001 PHE B 231 TYR 0.016 0.001 TYR A 306 ARG 0.002 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.697 Fit side-chains REVERT: A 108 HIS cc_start: 0.8307 (OUTLIER) cc_final: 0.7526 (t-90) REVERT: A 138 TYR cc_start: 0.8008 (m-80) cc_final: 0.7281 (m-80) REVERT: A 277 ARG cc_start: 0.7032 (mtt180) cc_final: 0.6590 (mmp-170) REVERT: A 348 MET cc_start: 0.8776 (mmm) cc_final: 0.8550 (mmm) REVERT: A 520 ILE cc_start: 0.9041 (mm) cc_final: 0.8759 (mt) REVERT: A 555 MET cc_start: 0.8377 (tpt) cc_final: 0.8097 (mmt) REVERT: A 773 MET cc_start: 0.9342 (mmm) cc_final: 0.8767 (tpp) REVERT: A 842 MET cc_start: 0.8181 (ttt) cc_final: 0.7822 (ttp) REVERT: A 851 PHE cc_start: 0.7624 (m-80) cc_final: 0.7352 (m-10) REVERT: B 47 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.7165 (t80) REVERT: B 108 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.7637 (t-90) REVERT: B 138 TYR cc_start: 0.8019 (m-80) cc_final: 0.7259 (m-80) REVERT: B 277 ARG cc_start: 0.6998 (mtt180) cc_final: 0.6596 (mmp-170) REVERT: B 522 MET cc_start: 0.7092 (mmm) cc_final: 0.6709 (mmm) REVERT: B 555 MET cc_start: 0.8404 (tpt) cc_final: 0.8096 (mmt) REVERT: B 557 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8271 (mp) REVERT: B 604 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7826 (tm-30) REVERT: B 773 MET cc_start: 0.9326 (mmm) cc_final: 0.8749 (tpp) REVERT: B 851 PHE cc_start: 0.7674 (m-80) cc_final: 0.7421 (m-10) outliers start: 36 outliers final: 24 residues processed: 171 average time/residue: 0.2202 time to fit residues: 57.0257 Evaluate side-chains 163 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 729 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 0.0970 chunk 69 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN B 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12488 Z= 0.180 Angle : 0.518 11.269 16928 Z= 0.264 Chirality : 0.040 0.143 1834 Planarity : 0.005 0.067 2100 Dihedral : 7.585 128.270 1676 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.96 % Allowed : 16.92 % Favored : 80.12 % 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: 1.18 (0.22), residues: 1434 helix: 1.76 (0.17), residues: 878 sheet: -0.25 (0.64), residues: 64 loop : -0.88 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 397 HIS 0.004 0.001 HIS A 830 PHE 0.023 0.001 PHE B 789 TYR 0.016 0.001 TYR A 855 ARG 0.001 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 138 time to evaluate : 1.414 Fit side-chains REVERT: A 93 LYS cc_start: 0.7796 (tppt) cc_final: 0.7590 (mtmt) REVERT: A 108 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.7563 (t-90) REVERT: A 138 TYR cc_start: 0.8014 (m-80) cc_final: 0.7281 (m-80) REVERT: A 277 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6607 (mmp-170) REVERT: A 348 MET cc_start: 0.8795 (mmm) cc_final: 0.8566 (mmm) REVERT: A 520 ILE cc_start: 0.9054 (mm) cc_final: 0.8807 (mt) REVERT: A 773 MET cc_start: 0.9314 (mmm) cc_final: 0.8748 (tpp) REVERT: A 842 MET cc_start: 0.8190 (ttt) cc_final: 0.7835 (ttp) REVERT: A 851 PHE cc_start: 0.7651 (m-80) cc_final: 0.7386 (m-10) REVERT: B 108 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.7658 (t-90) REVERT: B 138 TYR cc_start: 0.8037 (m-80) cc_final: 0.7299 (m-80) REVERT: B 277 ARG cc_start: 0.7016 (mtt180) cc_final: 0.6615 (mmp-170) REVERT: B 522 MET cc_start: 0.7118 (mmm) cc_final: 0.6733 (mmm) REVERT: B 557 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 773 MET cc_start: 0.9316 (mmm) cc_final: 0.8744 (tpp) REVERT: B 851 PHE cc_start: 0.7723 (m-80) cc_final: 0.7482 (m-10) outliers start: 39 outliers final: 26 residues processed: 167 average time/residue: 0.2056 time to fit residues: 52.7643 Evaluate side-chains 163 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 729 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 130 optimal weight: 0.1980 chunk 86 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN B 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12488 Z= 0.148 Angle : 0.501 11.485 16928 Z= 0.255 Chirality : 0.039 0.145 1834 Planarity : 0.005 0.067 2100 Dihedral : 7.460 127.563 1676 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.88 % Allowed : 17.15 % Favored : 79.97 % 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: 1.29 (0.22), residues: 1434 helix: 1.87 (0.17), residues: 878 sheet: -0.27 (0.64), residues: 64 loop : -0.85 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 397 HIS 0.003 0.000 HIS B 830 PHE 0.020 0.001 PHE B 789 TYR 0.017 0.001 TYR B 855 ARG 0.001 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 1.403 Fit side-chains REVERT: A 108 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7654 (t-90) REVERT: A 138 TYR cc_start: 0.7944 (m-80) cc_final: 0.7217 (m-80) REVERT: A 277 ARG cc_start: 0.7037 (mtt180) cc_final: 0.6587 (mmp-170) REVERT: A 348 MET cc_start: 0.8805 (mmm) cc_final: 0.8590 (mmm) REVERT: A 520 ILE cc_start: 0.9057 (mm) cc_final: 0.8819 (mt) REVERT: A 536 THR cc_start: 0.7790 (t) cc_final: 0.7273 (t) REVERT: A 773 MET cc_start: 0.9346 (mmm) cc_final: 0.8736 (tpp) REVERT: A 842 MET cc_start: 0.8168 (ttt) cc_final: 0.7806 (ttp) REVERT: A 851 PHE cc_start: 0.7626 (m-80) cc_final: 0.7368 (m-10) REVERT: B 93 LYS cc_start: 0.7996 (tppt) cc_final: 0.7793 (mttp) REVERT: B 108 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.7667 (t-90) REVERT: B 138 TYR cc_start: 0.7980 (m-80) cc_final: 0.7239 (m-80) REVERT: B 277 ARG cc_start: 0.7011 (mtt180) cc_final: 0.6591 (mmp-170) REVERT: B 522 MET cc_start: 0.7058 (mmm) cc_final: 0.6661 (mmm) REVERT: B 536 THR cc_start: 0.7755 (t) cc_final: 0.7258 (t) REVERT: B 773 MET cc_start: 0.9347 (mmm) cc_final: 0.8729 (tpp) REVERT: B 851 PHE cc_start: 0.7640 (m-80) cc_final: 0.7370 (m-10) outliers start: 38 outliers final: 32 residues processed: 166 average time/residue: 0.2187 time to fit residues: 54.9432 Evaluate side-chains 166 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 145 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN B 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12488 Z= 0.151 Angle : 0.505 12.086 16928 Z= 0.257 Chirality : 0.039 0.145 1834 Planarity : 0.005 0.067 2100 Dihedral : 7.439 127.328 1676 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.43 % Allowed : 17.91 % Favored : 79.67 % 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: 1.32 (0.22), residues: 1434 helix: 1.88 (0.17), residues: 878 sheet: -0.28 (0.65), residues: 64 loop : -0.81 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 650 HIS 0.003 0.000 HIS A 830 PHE 0.019 0.001 PHE B 789 TYR 0.017 0.001 TYR B 855 ARG 0.003 0.000 ARG B 810 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.324 Fit side-chains REVERT: A 93 LYS cc_start: 0.7973 (tppt) cc_final: 0.7635 (mtmt) REVERT: A 108 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7607 (t-90) REVERT: A 138 TYR cc_start: 0.7919 (m-80) cc_final: 0.7163 (m-80) REVERT: A 277 ARG cc_start: 0.7058 (mtt180) cc_final: 0.6604 (mmp-170) REVERT: A 348 MET cc_start: 0.8812 (mmm) cc_final: 0.8604 (mmm) REVERT: A 520 ILE cc_start: 0.9048 (mm) cc_final: 0.8810 (mt) REVERT: A 536 THR cc_start: 0.7680 (t) cc_final: 0.7391 (t) REVERT: A 773 MET cc_start: 0.9358 (mmm) cc_final: 0.8748 (tpp) REVERT: A 842 MET cc_start: 0.8139 (ttt) cc_final: 0.7692 (ttt) REVERT: A 851 PHE cc_start: 0.7625 (m-80) cc_final: 0.7367 (m-10) REVERT: B 108 HIS cc_start: 0.8312 (OUTLIER) cc_final: 0.7669 (t-90) REVERT: B 138 TYR cc_start: 0.7957 (m-80) cc_final: 0.7237 (m-80) REVERT: B 277 ARG cc_start: 0.7026 (mtt180) cc_final: 0.6610 (mmp-170) REVERT: B 522 MET cc_start: 0.7109 (mmm) cc_final: 0.6691 (mmm) REVERT: B 536 THR cc_start: 0.7611 (t) cc_final: 0.7295 (t) REVERT: B 773 MET cc_start: 0.9356 (mmm) cc_final: 0.8730 (tpp) REVERT: B 851 PHE cc_start: 0.7627 (m-80) cc_final: 0.7383 (m-10) outliers start: 32 outliers final: 29 residues processed: 157 average time/residue: 0.2121 time to fit residues: 50.6600 Evaluate side-chains 159 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.0070 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 119 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.0604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN B 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105793 restraints weight = 17353.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108127 restraints weight = 13465.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108953 restraints weight = 9969.324| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12488 Z= 0.253 Angle : 0.563 11.689 16928 Z= 0.288 Chirality : 0.041 0.143 1834 Planarity : 0.005 0.066 2100 Dihedral : 7.639 127.954 1676 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.58 % Allowed : 17.98 % Favored : 79.44 % 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: 1.05 (0.22), residues: 1434 helix: 1.67 (0.17), residues: 866 sheet: -0.40 (0.63), residues: 64 loop : -0.85 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 650 HIS 0.005 0.001 HIS A 830 PHE 0.025 0.002 PHE B 231 TYR 0.016 0.002 TYR B 855 ARG 0.003 0.000 ARG B 810 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2205.16 seconds wall clock time: 41 minutes 22.71 seconds (2482.71 seconds total)