Starting phenix.real_space_refine on Fri Feb 16 11:53:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8i_31020/02_2024/7e8i_31020.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8i_31020/02_2024/7e8i_31020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8i_31020/02_2024/7e8i_31020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8i_31020/02_2024/7e8i_31020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8i_31020/02_2024/7e8i_31020.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8i_31020/02_2024/7e8i_31020.pdb" } resolution = 3.1 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= 0.037 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 290 5.49 5 S 30 5.16 5 C 8711 2.51 5 N 2830 2.21 5 O 3410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H ARG 30": "NH1" <-> "NH2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "K GLU 478": "OE1" <-> "OE2" Residue "K GLU 587": "OE1" <-> "OE2" Residue "K GLU 649": "OE1" <-> "OE2" Residue "K GLU 655": "OE1" <-> "OE2" Residue "K ASP 689": "OD1" <-> "OD2" Residue "K ARG 731": "NH1" <-> "NH2" Residue "K GLU 748": "OE1" <-> "OE2" Residue "L ARG 42": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15271 Number of models: 1 Model: "" Number of chains: 12 Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 711 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "K" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2653 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 18, 'TRANS': 315} Chain breaks: 1 Chain: "L" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 8.54, per 1000 atoms: 0.56 Number of scatterers: 15271 At special positions: 0 Unit cell: (110, 116, 117, 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 30 16.00 P 290 15.00 O 3410 8.00 N 2830 7.00 C 8711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.59 Conformation dependent library (CDL) restraints added in 1.7 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2198 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 60.5% alpha, 4.6% beta 132 base pairs and 233 stacking pairs defined. Time for finding SS restraints: 7.03 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.508A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 114 removed outlier: 3.729A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.782A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.884A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.985A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.234A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.501A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.891A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.726A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.579A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.914A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.781A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.216A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.982A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.527A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.371A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.707A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.511A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 81 removed outlier: 3.549A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 99 removed outlier: 3.942A pdb=" N ALA H 94 " --> pdb=" O GLU H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.733A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 430 through 438 Processing helix chain 'K' and resid 440 through 449 Processing helix chain 'K' and resid 463 through 472 Processing helix chain 'K' and resid 474 through 483 Processing helix chain 'K' and resid 496 through 504 removed outlier: 3.535A pdb=" N ASP K 500 " --> pdb=" O SER K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 506 through 515 Processing helix chain 'K' and resid 530 through 535 removed outlier: 3.606A pdb=" N THR K 534 " --> pdb=" O PRO K 530 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP K 535 " --> pdb=" O VAL K 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 530 through 535' Processing helix chain 'K' and resid 536 through 544 removed outlier: 3.965A pdb=" N LEU K 544 " --> pdb=" O LYS K 540 " (cutoff:3.500A) Processing helix chain 'K' and resid 578 through 592 Processing helix chain 'K' and resid 617 through 627 Processing helix chain 'K' and resid 633 through 643 removed outlier: 3.938A pdb=" N LYS K 637 " --> pdb=" O PHE K 633 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG K 641 " --> pdb=" O LYS K 637 " (cutoff:3.500A) Processing helix chain 'K' and resid 655 through 666 Processing helix chain 'K' and resid 687 through 698 Processing helix chain 'K' and resid 711 through 716 removed outlier: 3.851A pdb=" N GLN K 715 " --> pdb=" O SER K 711 " (cutoff:3.500A) Processing helix chain 'K' and resid 760 through 770 removed outlier: 3.557A pdb=" N VAL K 767 " --> pdb=" O PHE K 763 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 30 removed outlier: 4.155A pdb=" N VAL L 26 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE L 30 " --> pdb=" O VAL L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 35 Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.503A pdb=" N GLN L 41 " --> pdb=" O PRO L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.691A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.652A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.386A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.993A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 572 through 574 removed outlier: 3.963A pdb=" N ILE K 573 " --> pdb=" O HIS K 606 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL K 608 " --> pdb=" O ILE K 573 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 701 through 702 removed outlier: 6.271A pdb=" N TYR K 676 " --> pdb=" O TYR K 736 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE K 738 " --> pdb=" O TYR K 676 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR K 678 " --> pdb=" O ILE K 738 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR K 739 " --> pdb=" O ALA K 758 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL K 755 " --> pdb=" O GLN K 752 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.749A pdb=" N LEU L 15 " --> pdb=" O ILE L 3 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE L 3 " --> pdb=" O LEU L 15 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU L 67 " --> pdb=" O GLN L 2 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE L 4 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU L 69 " --> pdb=" O PHE L 4 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS L 6 " --> pdb=" O LEU L 69 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 233 stacking parallelities Total time for adding SS restraints: 6.78 Time building geometry restraints manager: 8.03 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: 2016 1.32 - 1.44: 5597 1.44 - 1.57: 7908 1.57 - 1.69: 578 1.69 - 1.81: 46 Bond restraints: 16145 Sorted by residual: bond pdb=" CA SER D 61 " pdb=" CB SER D 61 " ideal model delta sigma weight residual 1.528 1.474 0.054 1.59e-02 3.96e+03 1.15e+01 bond pdb=" N ILE K 717 " pdb=" CA ILE K 717 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" CA SER D 57 " pdb=" CB SER D 57 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.56e-02 4.11e+03 1.08e+01 bond pdb=" CA SER D 53 " pdb=" CB SER D 53 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.05e+01 bond pdb=" CA SER H 75 " pdb=" CB SER H 75 " ideal model delta sigma weight residual 1.530 1.480 0.049 1.56e-02 4.11e+03 9.99e+00 ... (remaining 16140 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.62: 1495 105.62 - 112.71: 8900 112.71 - 119.79: 5528 119.79 - 126.88: 6321 126.88 - 133.96: 816 Bond angle restraints: 23060 Sorted by residual: angle pdb=" N TYR D 34 " pdb=" CA TYR D 34 " pdb=" C TYR D 34 " ideal model delta sigma weight residual 112.93 106.60 6.33 1.12e+00 7.97e-01 3.19e+01 angle pdb=" N LYS K 438 " pdb=" CA LYS K 438 " pdb=" C LYS K 438 " ideal model delta sigma weight residual 113.20 107.20 6.00 1.21e+00 6.83e-01 2.46e+01 angle pdb=" N LYS K 688 " pdb=" CA LYS K 688 " pdb=" C LYS K 688 " ideal model delta sigma weight residual 111.28 105.96 5.32 1.09e+00 8.42e-01 2.38e+01 angle pdb=" C PRO H 100 " pdb=" CA PRO H 100 " pdb=" CB PRO H 100 " ideal model delta sigma weight residual 111.56 104.00 7.56 1.65e+00 3.67e-01 2.10e+01 angle pdb=" N LEU H 103 " pdb=" CA LEU H 103 " pdb=" C LEU H 103 " ideal model delta sigma weight residual 111.07 106.24 4.83 1.07e+00 8.73e-01 2.04e+01 ... (remaining 23055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 7728 35.96 - 71.91: 1233 71.91 - 107.87: 12 107.87 - 143.82: 0 143.82 - 179.78: 4 Dihedral angle restraints: 8977 sinusoidal: 5571 harmonic: 3406 Sorted by residual: dihedral pdb=" CA HIS A 39 " pdb=" C HIS A 39 " pdb=" N ARG A 40 " pdb=" CA ARG A 40 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA ARG L 72 " pdb=" C ARG L 72 " pdb=" N LEU L 73 " pdb=" CA LEU L 73 " ideal model delta harmonic sigma weight residual 180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 39.78 -179.78 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2331 0.061 - 0.123: 207 0.123 - 0.184: 56 0.184 - 0.246: 20 0.246 - 0.307: 7 Chirality restraints: 2621 Sorted by residual: chirality pdb=" CA ILE K 737 " pdb=" N ILE K 737 " pdb=" C ILE K 737 " pdb=" CB ILE K 737 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA ILE C 102 " pdb=" N ILE C 102 " pdb=" C ILE C 102 " pdb=" CB ILE C 102 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA VAL B 21 " pdb=" N VAL B 21 " pdb=" C VAL B 21 " pdb=" CB VAL B 21 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2618 not shown) Planarity restraints: 1919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 33 " -0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C SER D 33 " 0.070 2.00e-02 2.50e+03 pdb=" O SER D 33 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR D 34 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 98 " 0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLY C 98 " -0.067 2.00e-02 2.50e+03 pdb=" O GLY C 98 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG C 99 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER K 711 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" C SER K 711 " -0.047 2.00e-02 2.50e+03 pdb=" O SER K 711 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP K 712 " 0.015 2.00e-02 2.50e+03 ... (remaining 1916 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1862 2.75 - 3.29: 13878 3.29 - 3.83: 29395 3.83 - 4.36: 35218 4.36 - 4.90: 50984 Nonbonded interactions: 131337 Sorted by model distance: nonbonded pdb=" OP2 DA J 21 " pdb=" OH TYR H 39 " model vdw 2.216 2.440 nonbonded pdb=" O LEU K 512 " pdb=" OG SER K 515 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.239 2.440 nonbonded pdb=" OP2 DG I 50 " pdb=" OG SER A 86 " model vdw 2.260 2.440 nonbonded pdb=" O SER D 120 " pdb=" OG SER D 120 " model vdw 2.311 2.440 ... (remaining 131332 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 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 19 through 101) selection = (chain 'F' and resid 19 through 101) } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 121) } 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: 1.190 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: 0.020 Extract box with map and model: 4.470 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 49.990 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.110 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.005 0.054 16145 Z= 0.295 Angle : 0.737 7.917 23060 Z= 0.511 Chirality : 0.047 0.307 2621 Planarity : 0.004 0.040 1919 Dihedral : 24.649 179.777 6779 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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: -2.84 (0.21), residues: 1154 helix: -1.38 (0.17), residues: 681 sheet: -2.67 (0.66), residues: 40 loop : -2.46 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 756 HIS 0.005 0.001 HIS E 39 PHE 0.012 0.001 PHE D 62 TYR 0.010 0.001 TYR K 736 ARG 0.004 0.000 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7875 (ttm110) REVERT: A 59 GLU cc_start: 0.8010 (pp20) cc_final: 0.7778 (pp20) REVERT: A 80 THR cc_start: 0.8939 (m) cc_final: 0.8732 (p) REVERT: C 99 ARG cc_start: 0.7768 (mmt180) cc_final: 0.7531 (mmm160) REVERT: E 56 LYS cc_start: 0.8493 (pttt) cc_final: 0.8148 (ptpt) REVERT: F 25 ASN cc_start: 0.7522 (m110) cc_final: 0.6969 (m110) REVERT: G 36 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7735 (ttpt) REVERT: G 73 ASN cc_start: 0.8599 (t0) cc_final: 0.7731 (t0) REVERT: G 74 LYS cc_start: 0.8704 (mptt) cc_final: 0.8214 (mtmt) REVERT: H 102 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7331 (mm-30) REVERT: K 618 LEU cc_start: 0.6517 (tt) cc_final: 0.5446 (pp) REVERT: L 40 GLN cc_start: 0.8031 (pt0) cc_final: 0.7061 (pp30) REVERT: L 63 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7634 (ptpp) REVERT: L 64 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8234 (mt-10) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3924 time to fit residues: 116.7471 Evaluate side-chains 168 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.0020 chunk 127 optimal weight: 0.4980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 104 GLN H 81 ASN K 521 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16145 Z= 0.182 Angle : 0.548 7.939 23060 Z= 0.316 Chirality : 0.035 0.163 2621 Planarity : 0.004 0.048 1919 Dihedral : 28.366 178.058 4459 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.90 % Allowed : 10.30 % Favored : 88.80 % 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: -1.33 (0.23), residues: 1154 helix: -0.04 (0.19), residues: 699 sheet: -2.36 (0.65), residues: 40 loop : -2.13 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 629 HIS 0.003 0.001 HIS D 46 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.001 TYR H 37 ARG 0.006 0.000 ARG K 520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 174 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8238 (mtt90) cc_final: 0.7989 (ttm110) REVERT: A 59 GLU cc_start: 0.8006 (pp20) cc_final: 0.7733 (pp20) REVERT: A 80 THR cc_start: 0.8840 (m) cc_final: 0.8531 (m) REVERT: B 77 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8204 (mmmt) REVERT: E 56 LYS cc_start: 0.8509 (pttt) cc_final: 0.8182 (ptpt) REVERT: G 36 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7728 (ttpt) REVERT: G 73 ASN cc_start: 0.8580 (t0) cc_final: 0.7638 (t0) REVERT: G 74 LYS cc_start: 0.8715 (mptt) cc_final: 0.8208 (mtmt) REVERT: H 105 LYS cc_start: 0.8297 (mtpt) cc_final: 0.8030 (ttmm) REVERT: K 486 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7782 (mp) REVERT: K 618 LEU cc_start: 0.6612 (tt) cc_final: 0.5606 (pp) REVERT: L 40 GLN cc_start: 0.8204 (pt0) cc_final: 0.7313 (pp30) REVERT: L 64 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8096 (mt-10) outliers start: 9 outliers final: 5 residues processed: 180 average time/residue: 0.3315 time to fit residues: 82.6174 Evaluate side-chains 167 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 161 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain K residue 486 LEU Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 49 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 113 optimal weight: 40.0000 chunk 126 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 108 ASN E 68 GLN K 521 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16145 Z= 0.377 Angle : 0.614 7.585 23060 Z= 0.349 Chirality : 0.040 0.162 2621 Planarity : 0.005 0.045 1919 Dihedral : 29.646 179.181 4459 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.00 % Allowed : 12.40 % Favored : 85.60 % 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: -0.83 (0.24), residues: 1154 helix: 0.33 (0.19), residues: 706 sheet: -2.15 (0.61), residues: 45 loop : -1.88 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 629 HIS 0.005 0.001 HIS D 46 PHE 0.015 0.002 PHE A 67 TYR 0.015 0.002 TYR G 57 ARG 0.005 0.001 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7955 (ttm110) REVERT: B 77 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8317 (mmmt) REVERT: B 84 MET cc_start: 0.7962 (tpp) cc_final: 0.7565 (tpt) REVERT: C 36 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8337 (tmtt) REVERT: E 56 LYS cc_start: 0.8578 (pttt) cc_final: 0.8219 (ptpt) REVERT: G 36 LYS cc_start: 0.8553 (ttmt) cc_final: 0.7876 (ttpt) REVERT: G 73 ASN cc_start: 0.8630 (t0) cc_final: 0.7666 (t0) REVERT: G 74 LYS cc_start: 0.8751 (mptt) cc_final: 0.8284 (mtmt) REVERT: H 56 MET cc_start: 0.8473 (tpp) cc_final: 0.8248 (mmm) REVERT: H 105 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8044 (ttmm) REVERT: K 684 LYS cc_start: 0.7745 (ptmt) cc_final: 0.7511 (ptmm) REVERT: K 701 GLN cc_start: 0.8379 (mp10) cc_final: 0.8040 (mp10) REVERT: L 40 GLN cc_start: 0.8145 (pt0) cc_final: 0.7839 (pp30) REVERT: L 64 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8307 (mt-10) outliers start: 20 outliers final: 13 residues processed: 180 average time/residue: 0.3296 time to fit residues: 82.8560 Evaluate side-chains 166 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 25 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 64 ASN E 68 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16145 Z= 0.233 Angle : 0.544 7.001 23060 Z= 0.316 Chirality : 0.036 0.147 2621 Planarity : 0.004 0.043 1919 Dihedral : 29.601 178.852 4459 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.10 % Allowed : 14.90 % Favored : 83.00 % 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: -0.21 (0.25), residues: 1154 helix: 0.83 (0.20), residues: 708 sheet: -2.06 (0.64), residues: 43 loop : -1.63 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 629 HIS 0.003 0.001 HIS D 46 PHE 0.008 0.001 PHE C 25 TYR 0.009 0.001 TYR K 446 ARG 0.007 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8310 (mtt90) cc_final: 0.7942 (ttm110) REVERT: B 49 LEU cc_start: 0.9120 (mt) cc_final: 0.8855 (mp) REVERT: B 77 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8218 (mmmt) REVERT: B 84 MET cc_start: 0.7846 (tpp) cc_final: 0.7587 (tpt) REVERT: C 36 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8308 (tmtt) REVERT: D 60 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7585 (t0) REVERT: E 56 LYS cc_start: 0.8565 (pttt) cc_final: 0.8202 (ptpt) REVERT: G 36 LYS cc_start: 0.8510 (ttmt) cc_final: 0.7866 (ttpt) REVERT: G 73 ASN cc_start: 0.8580 (t0) cc_final: 0.7674 (t0) REVERT: G 74 LYS cc_start: 0.8723 (mptt) cc_final: 0.8216 (mtmt) REVERT: H 105 LYS cc_start: 0.8287 (mtpt) cc_final: 0.8026 (ttmm) REVERT: K 701 GLN cc_start: 0.8318 (mp10) cc_final: 0.7830 (mp10) REVERT: L 40 GLN cc_start: 0.8219 (pt0) cc_final: 0.7984 (pp30) REVERT: L 60 ASN cc_start: 0.7874 (m110) cc_final: 0.7248 (p0) outliers start: 21 outliers final: 15 residues processed: 175 average time/residue: 0.3373 time to fit residues: 81.9271 Evaluate side-chains 171 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 487 VAL Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 25 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 0.0050 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 746 HIS ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16145 Z= 0.193 Angle : 0.529 5.925 23060 Z= 0.308 Chirality : 0.035 0.149 2621 Planarity : 0.004 0.043 1919 Dihedral : 29.503 178.753 4459 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.70 % Allowed : 15.90 % Favored : 82.40 % 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: 0.23 (0.25), residues: 1154 helix: 1.18 (0.20), residues: 709 sheet: -1.88 (0.63), residues: 44 loop : -1.46 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 629 HIS 0.002 0.001 HIS K 723 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR D 37 ARG 0.007 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8232 (mtt90) cc_final: 0.7928 (ttm110) REVERT: B 77 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8238 (mmmt) REVERT: C 33 LEU cc_start: 0.8860 (mt) cc_final: 0.8589 (mt) REVERT: C 104 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8219 (mm-40) REVERT: D 60 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7622 (t0) REVERT: E 56 LYS cc_start: 0.8562 (pttt) cc_final: 0.8197 (ptpt) REVERT: F 52 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7087 (mm-30) REVERT: G 36 LYS cc_start: 0.8511 (ttmt) cc_final: 0.7878 (ttpt) REVERT: G 73 ASN cc_start: 0.8568 (t0) cc_final: 0.7663 (t0) REVERT: G 74 LYS cc_start: 0.8739 (mptt) cc_final: 0.8238 (mtmt) REVERT: H 105 LYS cc_start: 0.8262 (mtpt) cc_final: 0.8002 (ttmm) REVERT: K 425 ASN cc_start: 0.8431 (t0) cc_final: 0.7949 (t0) REVERT: L 40 GLN cc_start: 0.8164 (pt0) cc_final: 0.6846 (pp30) REVERT: L 60 ASN cc_start: 0.7850 (m110) cc_final: 0.7188 (p0) REVERT: L 64 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8241 (mt-10) outliers start: 17 outliers final: 11 residues processed: 170 average time/residue: 0.3491 time to fit residues: 80.7494 Evaluate side-chains 166 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 487 VAL Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 30.0000 chunk 112 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16145 Z= 0.209 Angle : 0.543 6.925 23060 Z= 0.313 Chirality : 0.036 0.149 2621 Planarity : 0.004 0.043 1919 Dihedral : 29.539 177.998 4459 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.90 % Allowed : 16.50 % Favored : 81.60 % 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: 0.42 (0.25), residues: 1154 helix: 1.34 (0.20), residues: 706 sheet: -2.17 (0.61), residues: 47 loop : -1.31 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 629 HIS 0.002 0.001 HIS H 46 PHE 0.009 0.001 PHE A 67 TYR 0.015 0.001 TYR K 446 ARG 0.006 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7916 (ttm110) REVERT: B 77 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8221 (mmmt) REVERT: C 104 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8166 (mm-40) REVERT: D 60 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7641 (t0) REVERT: E 56 LYS cc_start: 0.8565 (pttt) cc_final: 0.8192 (ptpt) REVERT: G 36 LYS cc_start: 0.8508 (ttmt) cc_final: 0.7872 (ttpt) REVERT: G 73 ASN cc_start: 0.8565 (t0) cc_final: 0.7658 (t0) REVERT: G 74 LYS cc_start: 0.8742 (mptt) cc_final: 0.8226 (mtmt) REVERT: H 105 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7998 (ttmm) REVERT: K 425 ASN cc_start: 0.8391 (t0) cc_final: 0.8056 (t0) REVERT: K 621 MET cc_start: 0.7607 (mmp) cc_final: 0.7303 (mmm) REVERT: K 768 MET cc_start: 0.7536 (mmt) cc_final: 0.7273 (mmp) REVERT: L 11 LYS cc_start: 0.7181 (ttpt) cc_final: 0.6794 (pptt) REVERT: L 64 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8229 (mt-10) outliers start: 19 outliers final: 15 residues processed: 170 average time/residue: 0.3584 time to fit residues: 84.1810 Evaluate side-chains 170 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 487 VAL Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 32 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 83 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: ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16145 Z= 0.180 Angle : 0.529 7.037 23060 Z= 0.307 Chirality : 0.035 0.145 2621 Planarity : 0.004 0.043 1919 Dihedral : 29.438 177.871 4459 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.80 % Allowed : 16.60 % Favored : 81.60 % 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: 0.72 (0.25), residues: 1154 helix: 1.56 (0.20), residues: 705 sheet: -1.11 (0.69), residues: 38 loop : -1.30 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 629 HIS 0.002 0.000 HIS K 723 PHE 0.007 0.001 PHE A 67 TYR 0.015 0.001 TYR H 118 ARG 0.007 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8234 (mtt90) cc_final: 0.7906 (ttm110) REVERT: B 77 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8240 (mmmt) REVERT: C 104 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8116 (mm-40) REVERT: D 60 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7596 (t0) REVERT: E 42 ARG cc_start: 0.7271 (mtp85) cc_final: 0.6852 (mtp-110) REVERT: E 56 LYS cc_start: 0.8562 (pttt) cc_final: 0.8161 (ptpt) REVERT: F 52 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7132 (mm-30) REVERT: G 36 LYS cc_start: 0.8504 (ttmt) cc_final: 0.7866 (ttpt) REVERT: G 73 ASN cc_start: 0.8570 (t0) cc_final: 0.7653 (t0) REVERT: G 74 LYS cc_start: 0.8797 (mptt) cc_final: 0.8278 (mtmt) REVERT: H 105 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7946 (ttmm) REVERT: K 425 ASN cc_start: 0.8357 (t0) cc_final: 0.8038 (t0) REVERT: L 11 LYS cc_start: 0.7151 (ttpt) cc_final: 0.6762 (pptt) REVERT: L 64 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8186 (mt-10) outliers start: 18 outliers final: 15 residues processed: 169 average time/residue: 0.3460 time to fit residues: 81.1923 Evaluate side-chains 170 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 487 VAL Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 63 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16145 Z= 0.185 Angle : 0.536 7.870 23060 Z= 0.310 Chirality : 0.035 0.164 2621 Planarity : 0.004 0.042 1919 Dihedral : 29.436 177.724 4459 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.10 % Allowed : 16.50 % Favored : 81.40 % 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: 0.80 (0.25), residues: 1154 helix: 1.63 (0.20), residues: 705 sheet: -1.02 (0.70), residues: 38 loop : -1.28 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 629 HIS 0.003 0.001 HIS H 106 PHE 0.008 0.001 PHE A 67 TYR 0.015 0.001 TYR H 118 ARG 0.006 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8228 (mtt90) cc_final: 0.7904 (ttm110) REVERT: B 77 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8236 (mmmt) REVERT: C 104 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8100 (mm-40) REVERT: D 60 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7611 (t0) REVERT: E 42 ARG cc_start: 0.7233 (mtp85) cc_final: 0.6825 (mtp-110) REVERT: E 56 LYS cc_start: 0.8575 (pttt) cc_final: 0.8181 (ptpt) REVERT: G 36 LYS cc_start: 0.8504 (ttmt) cc_final: 0.7858 (ttpt) REVERT: G 73 ASN cc_start: 0.8566 (t0) cc_final: 0.7649 (t0) REVERT: G 74 LYS cc_start: 0.8815 (mptt) cc_final: 0.8284 (mtmt) REVERT: H 105 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7947 (ttmm) REVERT: K 425 ASN cc_start: 0.8357 (t0) cc_final: 0.8045 (t0) REVERT: K 537 GLU cc_start: 0.8157 (tp30) cc_final: 0.7887 (pm20) REVERT: L 11 LYS cc_start: 0.7234 (ttpt) cc_final: 0.6810 (pptt) REVERT: L 64 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8177 (mt-10) outliers start: 21 outliers final: 20 residues processed: 169 average time/residue: 0.3304 time to fit residues: 77.6597 Evaluate side-chains 172 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 487 VAL Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 63 LYS Chi-restraints excluded: chain L residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16145 Z= 0.190 Angle : 0.535 8.048 23060 Z= 0.309 Chirality : 0.035 0.173 2621 Planarity : 0.004 0.042 1919 Dihedral : 29.436 177.548 4459 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.30 % Allowed : 16.20 % Favored : 81.50 % 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: 0.87 (0.25), residues: 1154 helix: 1.69 (0.20), residues: 705 sheet: -0.95 (0.71), residues: 38 loop : -1.27 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 629 HIS 0.002 0.001 HIS K 723 PHE 0.009 0.001 PHE K 600 TYR 0.014 0.001 TYR H 118 ARG 0.007 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8227 (mtt90) cc_final: 0.7896 (ttm110) REVERT: B 49 LEU cc_start: 0.8812 (mt) cc_final: 0.8568 (mp) REVERT: B 77 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8238 (mmmt) REVERT: D 60 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7611 (t0) REVERT: E 56 LYS cc_start: 0.8579 (pttt) cc_final: 0.8186 (ptpt) REVERT: E 94 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7672 (mm-30) REVERT: G 36 LYS cc_start: 0.8496 (ttmt) cc_final: 0.7861 (ttpt) REVERT: G 73 ASN cc_start: 0.8567 (t0) cc_final: 0.7651 (t0) REVERT: G 74 LYS cc_start: 0.8824 (mptt) cc_final: 0.8303 (mtmt) REVERT: H 105 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7945 (ttmm) REVERT: K 425 ASN cc_start: 0.8368 (t0) cc_final: 0.8050 (t0) REVERT: K 537 GLU cc_start: 0.8158 (tp30) cc_final: 0.7887 (pm20) REVERT: L 11 LYS cc_start: 0.7251 (ttpt) cc_final: 0.6791 (pptt) REVERT: L 64 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8166 (mt-10) outliers start: 23 outliers final: 20 residues processed: 173 average time/residue: 0.3456 time to fit residues: 82.6514 Evaluate side-chains 177 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 487 VAL Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 63 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16145 Z= 0.207 Angle : 0.545 10.483 23060 Z= 0.313 Chirality : 0.035 0.180 2621 Planarity : 0.004 0.042 1919 Dihedral : 29.457 177.338 4459 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.30 % Allowed : 15.80 % Favored : 81.90 % 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: 0.87 (0.25), residues: 1154 helix: 1.68 (0.20), residues: 706 sheet: -0.94 (0.70), residues: 38 loop : -1.27 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 629 HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.014 0.001 TYR H 118 ARG 0.007 0.000 ARG L 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8208 (mtt90) cc_final: 0.7872 (ttm110) REVERT: B 49 LEU cc_start: 0.8787 (mt) cc_final: 0.8552 (mp) REVERT: B 77 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8228 (mmmt) REVERT: D 60 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7610 (t0) REVERT: E 42 ARG cc_start: 0.7287 (mtp85) cc_final: 0.6892 (mtp-110) REVERT: E 56 LYS cc_start: 0.8583 (pttt) cc_final: 0.8189 (ptpt) REVERT: G 36 LYS cc_start: 0.8499 (ttmt) cc_final: 0.7857 (ttpt) REVERT: G 73 ASN cc_start: 0.8570 (t0) cc_final: 0.7656 (t0) REVERT: G 74 LYS cc_start: 0.8828 (mptt) cc_final: 0.8307 (mtmt) REVERT: H 105 LYS cc_start: 0.8256 (mtpt) cc_final: 0.8002 (ttmm) REVERT: K 425 ASN cc_start: 0.8367 (t0) cc_final: 0.8055 (t0) REVERT: K 537 GLU cc_start: 0.8161 (tp30) cc_final: 0.7892 (pm20) REVERT: L 11 LYS cc_start: 0.7252 (ttpt) cc_final: 0.6793 (pptt) REVERT: L 64 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8140 (mt-10) outliers start: 23 outliers final: 19 residues processed: 170 average time/residue: 0.3364 time to fit residues: 79.8913 Evaluate side-chains 173 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 487 VAL Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 727 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 63 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.162264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099367 restraints weight = 20948.342| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.14 r_work: 0.3059 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16145 Z= 0.248 Angle : 0.559 8.309 23060 Z= 0.321 Chirality : 0.037 0.159 2621 Planarity : 0.004 0.042 1919 Dihedral : 29.678 176.325 4459 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.10 % Allowed : 16.20 % Favored : 81.70 % 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: 0.75 (0.25), residues: 1154 helix: 1.56 (0.20), residues: 707 sheet: -0.90 (0.71), residues: 38 loop : -1.28 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 629 HIS 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.015 0.001 TYR H 118 ARG 0.007 0.000 ARG H 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.94 seconds wall clock time: 55 minutes 29.50 seconds (3329.50 seconds total)