Starting phenix.real_space_refine on Thu Mar 14 15:47:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/03_2024/7v07_26940_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/03_2024/7v07_26940.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/03_2024/7v07_26940_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/03_2024/7v07_26940_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/03_2024/7v07_26940_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/03_2024/7v07_26940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/03_2024/7v07_26940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/03_2024/7v07_26940_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/03_2024/7v07_26940_updated.pdb" } resolution = 2.8 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= 0.001 sd= 0.162 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 8 5.49 5 S 38 5.16 5 C 6134 2.51 5 N 1410 2.21 5 O 1572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C GLU 480": "OE1" <-> "OE2" Residue "C PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 535": "OE1" <-> "OE2" Residue "C PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 621": "OD1" <-> "OD2" Residue "C PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 755": "OE1" <-> "OE2" Residue "C TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 889": "OD1" <-> "OD2" Residue "E ASP 385": "OD1" <-> "OD2" Residue "E ASP 396": "OD1" <-> "OD2" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "E PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 485": "OE1" <-> "OE2" Residue "E PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 522": "OE1" <-> "OE2" Residue "E GLU 535": "OE1" <-> "OE2" Residue "E ASP 546": "OD1" <-> "OD2" Residue "E TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 621": "OD1" <-> "OD2" Residue "E GLU 681": "OE1" <-> "OE2" Residue "E GLU 882": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9162 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'CLR': 2, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 192 Unusual residues: {'CLR': 2, 'PIO': 2, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.65, per 1000 atoms: 0.62 Number of scatterers: 9162 At special positions: 0 Unit cell: (142.345, 86.735, 115.785, 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 38 16.00 P 8 15.00 O 1572 8.00 N 1410 7.00 C 6134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA A 3 " - " MAN A 4 " " BMA F 3 " - " MAN F 4 " ALPHA1-4 " BMA A 3 " - " MAN A 5 " " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " BETA1-6 " NAG A 1 " - " FUC A 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 6 " NAG-ASN " NAG A 1 " - " ASN C 642 " " NAG F 1 " - " ASN E 642 " Time building additional restraints: 4.42 Conformation dependent library (CDL) restraints added in 1.3 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 2 sheets defined 66.5% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'D' and resid 89 through 113 Processing helix chain 'C' and resid 380 through 393 removed outlier: 3.536A pdb=" N ARG C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Proline residue: C 391 - end of helix Processing helix chain 'C' and resid 395 through 400 removed outlier: 5.133A pdb=" N ALA C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 431 removed outlier: 3.636A pdb=" N PHE C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 437 through 454 Processing helix chain 'C' and resid 466 through 481 Processing helix chain 'C' and resid 486 through 506 removed outlier: 3.626A pdb=" N LEU C 499 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 Processing helix chain 'C' and resid 518 through 546 Processing helix chain 'C' and resid 570 through 593 removed outlier: 3.638A pdb=" N ASN C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 609 through 623 Processing helix chain 'C' and resid 661 through 689 removed outlier: 3.582A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ALA C 668 " --> pdb=" O MET C 664 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU C 669 " --> pdb=" O PHE C 665 " (cutoff:3.500A) Proline residue: C 670 - end of helix Processing helix chain 'C' and resid 692 through 694 No H-bonds generated for 'chain 'C' and resid 692 through 694' Processing helix chain 'C' and resid 704 through 719 removed outlier: 3.751A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 719 " --> pdb=" O VAL C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 737 Processing helix chain 'C' and resid 761 through 774 removed outlier: 4.826A pdb=" N ILE C 774 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 782 removed outlier: 4.618A pdb=" N ARG C 782 " --> pdb=" O PRO C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 800 removed outlier: 4.111A pdb=" N LEU C 800 " --> pdb=" O GLY C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 812 Processing helix chain 'C' and resid 823 through 826 No H-bonds generated for 'chain 'C' and resid 823 through 826' Processing helix chain 'C' and resid 830 through 852 Processing helix chain 'C' and resid 856 through 871 removed outlier: 3.501A pdb=" N LEU C 859 " --> pdb=" O SER C 856 " (cutoff:3.500A) Proline residue: C 860 - end of helix Proline residue: C 868 - end of helix Processing helix chain 'C' and resid 873 through 877 removed outlier: 3.746A pdb=" N ILE C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 873 through 877' Processing helix chain 'C' and resid 880 through 886 Processing helix chain 'E' and resid 380 through 400 Proline residue: E 391 - end of helix removed outlier: 5.214A pdb=" N LEU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N SER E 395 " --> pdb=" O PRO E 391 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 431 Proline residue: E 419 - end of helix Processing helix chain 'E' and resid 437 through 454 Processing helix chain 'E' and resid 466 through 482 Processing helix chain 'E' and resid 486 through 506 removed outlier: 3.541A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 515 removed outlier: 3.560A pdb=" N LEU E 512 " --> pdb=" O GLY E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 546 removed outlier: 3.642A pdb=" N LEU E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 592 Processing helix chain 'E' and resid 599 through 607 Processing helix chain 'E' and resid 609 through 623 Processing helix chain 'E' and resid 661 through 689 removed outlier: 3.825A pdb=" N PHE E 665 " --> pdb=" O ILE E 661 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA E 668 " --> pdb=" O MET E 664 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU E 669 " --> pdb=" O PHE E 665 " (cutoff:3.500A) Proline residue: E 670 - end of helix Processing helix chain 'E' and resid 692 through 694 No H-bonds generated for 'chain 'E' and resid 692 through 694' Processing helix chain 'E' and resid 704 through 718 removed outlier: 3.752A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 728 through 737 Processing helix chain 'E' and resid 761 through 774 removed outlier: 4.762A pdb=" N ILE E 774 " --> pdb=" O VAL E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 782 removed outlier: 4.143A pdb=" N ARG E 782 " --> pdb=" O PRO E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 800 removed outlier: 4.066A pdb=" N LEU E 800 " --> pdb=" O GLY E 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 804 through 813 removed outlier: 4.041A pdb=" N PHE E 813 " --> pdb=" O ILE E 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 823 through 826 No H-bonds generated for 'chain 'E' and resid 823 through 826' Processing helix chain 'E' and resid 830 through 851 Processing helix chain 'E' and resid 856 through 871 Proline residue: E 860 - end of helix Proline residue: E 868 - end of helix Processing helix chain 'E' and resid 874 through 877 No H-bonds generated for 'chain 'E' and resid 874 through 877' Processing helix chain 'E' and resid 880 through 886 Processing sheet with id= A, first strand: chain 'C' and resid 739 through 741 Processing sheet with id= B, first strand: chain 'E' and resid 739 through 741 496 hydrogen bonds defined for protein. 1428 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: 2.55 Time building geometry restraints manager: 4.68 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: 1318 1.32 - 1.44: 2473 1.44 - 1.56: 5510 1.56 - 1.69: 17 1.69 - 1.81: 70 Bond restraints: 9388 Sorted by residual: bond pdb=" C PRO E 815 " pdb=" O PRO E 815 " ideal model delta sigma weight residual 1.246 1.195 0.051 8.50e-03 1.38e+04 3.54e+01 bond pdb=" C PRO C 815 " pdb=" O PRO C 815 " ideal model delta sigma weight residual 1.246 1.196 0.049 8.50e-03 1.38e+04 3.38e+01 bond pdb=" N VAL C 560 " pdb=" CA VAL C 560 " ideal model delta sigma weight residual 1.457 1.497 -0.040 9.00e-03 1.23e+04 1.99e+01 bond pdb=" C1 MAN A 4 " pdb=" C2 MAN A 4 " ideal model delta sigma weight residual 1.526 1.601 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1B PIO E1004 " pdb=" O3C PIO E1004 " ideal model delta sigma weight residual 1.399 1.326 0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 9383 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.90: 267 105.90 - 112.93: 5204 112.93 - 119.97: 3374 119.97 - 127.00: 3841 127.00 - 134.04: 88 Bond angle restraints: 12774 Sorted by residual: angle pdb=" C ARG D 80 " pdb=" CA ARG D 80 " pdb=" CB ARG D 80 " ideal model delta sigma weight residual 116.54 109.97 6.57 1.15e+00 7.56e-01 3.26e+01 angle pdb=" C TYR C 818 " pdb=" CA TYR C 818 " pdb=" CB TYR C 818 " ideal model delta sigma weight residual 110.79 119.42 -8.63 1.66e+00 3.63e-01 2.70e+01 angle pdb=" N PRO C 598 " pdb=" CA PRO C 598 " pdb=" C PRO C 598 " ideal model delta sigma weight residual 111.14 103.04 8.10 1.56e+00 4.11e-01 2.69e+01 angle pdb=" N GLN E 434 " pdb=" CA GLN E 434 " pdb=" C GLN E 434 " ideal model delta sigma weight residual 111.28 105.84 5.44 1.09e+00 8.42e-01 2.49e+01 angle pdb=" N PRO C 568 " pdb=" CA PRO C 568 " pdb=" C PRO C 568 " ideal model delta sigma weight residual 111.21 118.32 -7.11 1.59e+00 3.96e-01 2.00e+01 ... (remaining 12769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.96: 5255 25.96 - 51.92: 485 51.92 - 77.88: 79 77.88 - 103.85: 46 103.85 - 129.81: 17 Dihedral angle restraints: 5882 sinusoidal: 2680 harmonic: 3202 Sorted by residual: dihedral pdb=" C2 MAN F 5 " pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " pdb=" C5 MAN F 5 " ideal model delta sinusoidal sigma weight residual -57.62 72.19 -129.81 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C TYR C 818 " pdb=" N TYR C 818 " pdb=" CA TYR C 818 " pdb=" CB TYR C 818 " ideal model delta harmonic sigma weight residual -122.60 -132.98 10.38 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" C2 MAN A 5 " pdb=" C1 MAN A 5 " pdb=" O5 MAN A 5 " pdb=" C5 MAN A 5 " ideal model delta sinusoidal sigma weight residual -57.62 66.85 -124.47 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 5879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1323 0.074 - 0.147: 193 0.147 - 0.221: 34 0.221 - 0.294: 9 0.294 - 0.368: 3 Chirality restraints: 1562 Sorted by residual: chirality pdb=" C1 MAN A 5 " pdb=" O4 BMA A 3 " pdb=" C2 MAN A 5 " pdb=" O5 MAN A 5 " both_signs ideal model delta sigma weight residual False 2.40 2.03 0.37 2.00e-02 2.50e+03 3.39e+02 chirality pdb=" C1 MAN F 5 " pdb=" O4 BMA F 3 " pdb=" C2 MAN F 5 " pdb=" O5 MAN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.17 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" CA LYS C 817 " pdb=" N LYS C 817 " pdb=" C LYS C 817 " pdb=" CB LYS C 817 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 1559 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 874 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO E 875 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO E 875 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 875 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 470 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C VAL C 470 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL C 470 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE C 471 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 429 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C GLU E 429 " -0.058 2.00e-02 2.50e+03 pdb=" O GLU E 429 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS E 430 " 0.019 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1939 2.78 - 3.31: 8922 3.31 - 3.84: 16022 3.84 - 4.37: 19092 4.37 - 4.90: 31497 Nonbonded interactions: 77472 Sorted by model distance: nonbonded pdb=" OG1 THR C 375 " pdb=" OE2 GLU C 508 " model vdw 2.251 2.440 nonbonded pdb=" OG SER C 529 " pdb=" OG SER C 799 " model vdw 2.273 2.440 nonbonded pdb=" OD2 ASP C 636 " pdb=" NZ LYS C 639 " model vdw 2.296 2.520 nonbonded pdb=" O SER C 644 " pdb=" NH2 ARG C 656 " model vdw 2.313 2.520 nonbonded pdb=" OG SER C 438 " pdb=" OE2 GLU C 439 " model vdw 2.322 2.440 ... (remaining 77467 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 'F' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 371 through 894 or resid 1001 through 1003)) } 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: 1.920 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: 11.510 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 28.700 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.007 0.079 9388 Z= 0.447 Angle : 0.997 10.460 12774 Z= 0.617 Chirality : 0.058 0.368 1562 Planarity : 0.007 0.093 1498 Dihedral : 21.787 129.806 3818 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.81 % Favored : 97.91 % Rotamer: Outliers : 3.89 % Allowed : 20.53 % Favored : 75.58 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.45 % 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: 1.10 (0.24), residues: 1102 helix: 1.16 (0.18), residues: 744 sheet: None (None), residues: 0 loop : -0.02 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 492 HIS 0.002 0.000 HIS E 834 PHE 0.013 0.001 PHE B 87 TYR 0.028 0.002 TYR C 818 ARG 0.010 0.001 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 0.985 Fit side-chains REVERT: C 439 GLU cc_start: 0.8841 (mp0) cc_final: 0.8352 (mm-30) REVERT: C 557 VAL cc_start: 0.6589 (OUTLIER) cc_final: 0.6327 (m) REVERT: C 590 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7733 (mtpm) REVERT: C 592 LYS cc_start: 0.8184 (tttm) cc_final: 0.7769 (ttpt) REVERT: E 435 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9095 (mtp) REVERT: E 625 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: E 826 LYS cc_start: 0.7635 (mmtt) cc_final: 0.7360 (mmtp) outliers start: 37 outliers final: 16 residues processed: 206 average time/residue: 1.0874 time to fit residues: 240.3898 Evaluate side-chains 186 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain E residue 405 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 672 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN ** E 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9388 Z= 0.191 Angle : 0.578 8.283 12774 Z= 0.274 Chirality : 0.044 0.287 1562 Planarity : 0.006 0.072 1498 Dihedral : 19.505 115.125 1835 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.95 % Allowed : 19.26 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.70 (0.24), residues: 1102 helix: 1.68 (0.18), residues: 742 sheet: None (None), residues: 0 loop : 0.09 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 831 HIS 0.002 0.001 HIS E 834 PHE 0.017 0.001 PHE C 836 TYR 0.011 0.001 TYR C 824 ARG 0.005 0.000 ARG C 827 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 177 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: C 551 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7651 (tmtm) REVERT: C 564 GLN cc_start: 0.7431 (mm110) cc_final: 0.7177 (mm110) REVERT: C 590 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7721 (mtpm) REVERT: C 592 LYS cc_start: 0.8379 (tttm) cc_final: 0.7916 (ttpt) REVERT: E 435 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8974 (mtp) REVERT: E 541 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8631 (mt) REVERT: E 603 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7603 (mtt-85) REVERT: E 625 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.6045 (tm-30) REVERT: E 826 LYS cc_start: 0.7802 (mmtt) cc_final: 0.7602 (mmtm) outliers start: 47 outliers final: 20 residues processed: 198 average time/residue: 1.1313 time to fit residues: 240.0773 Evaluate side-chains 202 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 856 SER Chi-restraints excluded: chain E residue 864 ILE Chi-restraints excluded: chain E residue 877 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 564 GLN C 884 GLN E 569 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9388 Z= 0.279 Angle : 0.606 9.696 12774 Z= 0.286 Chirality : 0.045 0.261 1562 Planarity : 0.006 0.069 1498 Dihedral : 18.544 115.476 1818 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.58 % Allowed : 19.26 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.59 (0.24), residues: 1102 helix: 1.53 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.15 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 492 HIS 0.003 0.001 HIS E 834 PHE 0.020 0.002 PHE C 836 TYR 0.012 0.002 TYR E 824 ARG 0.002 0.000 ARG E 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 174 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: C 551 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7706 (tmtm) REVERT: C 759 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.7037 (pp30) REVERT: C 827 ARG cc_start: 0.8321 (mtp85) cc_final: 0.8091 (mtp-110) REVERT: E 541 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8662 (mt) REVERT: E 759 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.7875 (pp30) REVERT: E 826 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7755 (mmtm) outliers start: 53 outliers final: 20 residues processed: 197 average time/residue: 1.1482 time to fit residues: 242.2059 Evaluate side-chains 193 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 885 CYS Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9388 Z= 0.231 Angle : 0.573 9.996 12774 Z= 0.268 Chirality : 0.044 0.242 1562 Planarity : 0.006 0.065 1498 Dihedral : 17.537 113.972 1809 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.26 % Allowed : 20.00 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.73 (0.24), residues: 1102 helix: 1.62 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.28 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 492 HIS 0.002 0.001 HIS C 734 PHE 0.018 0.001 PHE C 836 TYR 0.011 0.002 TYR C 486 ARG 0.002 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 171 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: C 503 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8103 (mp) REVERT: C 551 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7682 (tmtm) REVERT: C 693 GLU cc_start: 0.7258 (pt0) cc_final: 0.7009 (pm20) REVERT: C 759 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.7003 (pp30) REVERT: C 827 ARG cc_start: 0.8304 (mtp85) cc_final: 0.8065 (mtp-110) REVERT: E 430 LYS cc_start: 0.8805 (mttm) cc_final: 0.8475 (mtmt) REVERT: E 759 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.7856 (pp30) REVERT: E 826 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7788 (mmtm) outliers start: 50 outliers final: 21 residues processed: 196 average time/residue: 1.2217 time to fit residues: 255.8813 Evaluate side-chains 204 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 697 VAL Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 856 SER Chi-restraints excluded: chain E residue 864 ILE Chi-restraints excluded: chain E residue 877 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 564 GLN C 880 ASN E 569 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9388 Z= 0.277 Angle : 0.597 9.889 12774 Z= 0.280 Chirality : 0.045 0.253 1562 Planarity : 0.006 0.062 1498 Dihedral : 17.040 113.786 1809 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.89 % Allowed : 19.58 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.24), residues: 1102 helix: 1.53 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.31 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 492 HIS 0.002 0.001 HIS C 734 PHE 0.018 0.002 PHE C 836 TYR 0.013 0.002 TYR E 824 ARG 0.006 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 178 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: D 107 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7787 (mp) REVERT: C 480 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: C 503 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8133 (mp) REVERT: C 551 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7759 (mmtm) REVERT: C 759 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.7051 (pp30) REVERT: C 810 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8567 (mp) REVERT: E 430 LYS cc_start: 0.8803 (mttm) cc_final: 0.8474 (mtmt) REVERT: E 541 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8660 (mt) REVERT: E 759 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.7963 (pp30) outliers start: 56 outliers final: 24 residues processed: 207 average time/residue: 1.1394 time to fit residues: 252.2828 Evaluate side-chains 202 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 170 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 697 VAL Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 762 SER Chi-restraints excluded: chain E residue 856 SER Chi-restraints excluded: chain E residue 864 ILE Chi-restraints excluded: chain E residue 889 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 0.0000 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 651 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9388 Z= 0.174 Angle : 0.543 9.754 12774 Z= 0.253 Chirality : 0.043 0.268 1562 Planarity : 0.005 0.059 1498 Dihedral : 16.300 113.374 1809 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.63 % Allowed : 20.95 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.25), residues: 1102 helix: 1.75 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.37 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 492 HIS 0.002 0.000 HIS C 547 PHE 0.016 0.001 PHE C 836 TYR 0.011 0.001 TYR C 486 ARG 0.005 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 179 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: C 480 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: C 551 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7678 (tmtm) REVERT: C 639 LYS cc_start: 0.8030 (mttt) cc_final: 0.7799 (ptpp) REVERT: E 394 LEU cc_start: 0.8109 (tt) cc_final: 0.7885 (mp) REVERT: E 430 LYS cc_start: 0.8769 (mttm) cc_final: 0.8417 (mtmt) REVERT: E 656 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.6955 (mtt90) REVERT: E 658 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7041 (tt0) outliers start: 44 outliers final: 18 residues processed: 200 average time/residue: 1.0859 time to fit residues: 232.7344 Evaluate side-chains 205 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 656 ARG Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 864 ILE Chi-restraints excluded: chain E residue 877 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN E 434 GLN E 569 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9388 Z= 0.286 Angle : 0.607 9.635 12774 Z= 0.284 Chirality : 0.045 0.269 1562 Planarity : 0.006 0.059 1498 Dihedral : 15.904 113.027 1809 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.16 % Allowed : 20.63 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.68 (0.25), residues: 1102 helix: 1.55 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.33 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 492 HIS 0.002 0.001 HIS C 734 PHE 0.018 0.002 PHE C 836 TYR 0.013 0.002 TYR E 824 ARG 0.013 0.001 ARG C 827 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 175 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: C 503 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8095 (mp) REVERT: C 551 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7762 (mmtm) REVERT: C 759 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.7033 (pp30) REVERT: C 810 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8592 (mp) REVERT: C 827 ARG cc_start: 0.8312 (mtp85) cc_final: 0.8007 (mtp-110) REVERT: E 394 LEU cc_start: 0.8152 (tt) cc_final: 0.7902 (mp) REVERT: E 430 LYS cc_start: 0.8774 (mttm) cc_final: 0.8430 (mtmt) REVERT: E 541 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8660 (mt) REVERT: E 759 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.7858 (pp30) REVERT: E 826 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7773 (mmtm) outliers start: 49 outliers final: 26 residues processed: 199 average time/residue: 1.1922 time to fit residues: 253.0859 Evaluate side-chains 208 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 885 CYS Chi-restraints excluded: chain E residue 434 GLN Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 697 VAL Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 856 SER Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9388 Z= 0.198 Angle : 0.567 9.548 12774 Z= 0.264 Chirality : 0.043 0.267 1562 Planarity : 0.005 0.058 1498 Dihedral : 15.393 112.713 1809 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.05 % Allowed : 20.74 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.84 (0.25), residues: 1102 helix: 1.69 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.35 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 492 HIS 0.002 0.000 HIS C 547 PHE 0.016 0.001 PHE C 836 TYR 0.011 0.001 TYR C 486 ARG 0.009 0.000 ARG C 827 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 181 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: C 503 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8089 (mp) REVERT: C 551 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7746 (mmtm) REVERT: C 759 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.6976 (pp30) REVERT: C 827 ARG cc_start: 0.8267 (mtp85) cc_final: 0.8062 (mtp-110) REVERT: E 394 LEU cc_start: 0.8121 (tt) cc_final: 0.7894 (mp) REVERT: E 430 LYS cc_start: 0.8758 (mttm) cc_final: 0.8411 (mtmt) REVERT: E 434 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: E 541 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8650 (mt) REVERT: E 656 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7013 (mtt90) REVERT: E 658 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7022 (tt0) outliers start: 48 outliers final: 23 residues processed: 204 average time/residue: 1.1940 time to fit residues: 260.4153 Evaluate side-chains 206 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 434 GLN Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 656 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 697 VAL Chi-restraints excluded: chain E residue 856 SER Chi-restraints excluded: chain E residue 864 ILE Chi-restraints excluded: chain E residue 889 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.2980 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 0.1980 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN E 434 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9388 Z= 0.154 Angle : 0.548 9.583 12774 Z= 0.251 Chirality : 0.042 0.248 1562 Planarity : 0.005 0.056 1498 Dihedral : 14.389 112.056 1809 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.74 % Allowed : 23.16 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.99 (0.25), residues: 1102 helix: 1.85 (0.19), residues: 748 sheet: None (None), residues: 0 loop : 0.28 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 492 HIS 0.001 0.000 HIS C 547 PHE 0.015 0.001 PHE C 836 TYR 0.011 0.001 TYR C 486 ARG 0.009 0.000 ARG C 827 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: C 535 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7997 (mm-30) REVERT: C 592 LYS cc_start: 0.8421 (tttm) cc_final: 0.7837 (ttpt) REVERT: E 430 LYS cc_start: 0.8743 (mttm) cc_final: 0.8385 (mtmt) REVERT: E 625 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: E 656 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.6962 (mtt90) REVERT: E 658 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7037 (tt0) outliers start: 26 outliers final: 15 residues processed: 201 average time/residue: 1.1625 time to fit residues: 249.7830 Evaluate side-chains 202 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 434 GLN Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 656 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 884 GLN E 569 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9388 Z= 0.254 Angle : 0.589 9.192 12774 Z= 0.275 Chirality : 0.044 0.232 1562 Planarity : 0.006 0.056 1498 Dihedral : 14.133 111.614 1809 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.32 % Allowed : 23.89 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.87 (0.25), residues: 1102 helix: 1.73 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.33 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 492 HIS 0.002 0.000 HIS C 734 PHE 0.018 0.001 PHE C 836 TYR 0.013 0.002 TYR E 824 ARG 0.007 0.000 ARG E 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 177 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: C 551 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7782 (mmtm) REVERT: C 592 LYS cc_start: 0.8482 (tttm) cc_final: 0.7884 (ttpt) REVERT: E 430 LYS cc_start: 0.8744 (mttm) cc_final: 0.8395 (mtmt) REVERT: E 625 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: E 658 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7037 (tt0) outliers start: 22 outliers final: 15 residues processed: 186 average time/residue: 1.2392 time to fit residues: 245.4392 Evaluate side-chains 193 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 856 SER Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 884 GLN E 434 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.139763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.117486 restraints weight = 10246.614| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.36 r_work: 0.3097 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9388 Z= 0.155 Angle : 0.547 10.115 12774 Z= 0.253 Chirality : 0.041 0.178 1562 Planarity : 0.005 0.057 1498 Dihedral : 13.349 110.980 1809 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.21 % Allowed : 24.53 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.07 (0.25), residues: 1102 helix: 1.91 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 0.35 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 492 HIS 0.001 0.000 HIS C 819 PHE 0.015 0.001 PHE C 836 TYR 0.011 0.001 TYR C 486 ARG 0.011 0.000 ARG C 827 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4268.83 seconds wall clock time: 75 minutes 48.51 seconds (4548.51 seconds total)