Starting phenix.real_space_refine on Sat Mar 16 07:36:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieg_35381/03_2024/8ieg_35381.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieg_35381/03_2024/8ieg_35381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieg_35381/03_2024/8ieg_35381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieg_35381/03_2024/8ieg_35381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieg_35381/03_2024/8ieg_35381.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieg_35381/03_2024/8ieg_35381.pdb" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 294 5.49 5 S 41 5.16 5 C 7940 2.51 5 N 2632 2.21 5 O 3191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L ASP 85": "OD1" <-> "OD2" Residue "L PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 681": "NH1" <-> "NH2" 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: 14102 Number of models: 1 Model: "" Number of chains: 15 Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "L" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 502 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 489 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 61} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1062 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12259 SG CYS A 663 52.674 64.189 27.278 1.00128.54 S ATOM 12418 SG CYS A 683 55.929 65.875 27.316 1.00 99.25 S ATOM 12438 SG CYS A 686 52.822 68.039 26.747 1.00114.54 S ATOM 12142 SG CYS A 648 63.679 58.375 26.869 1.00158.80 S ATOM 12162 SG CYS A 651 66.888 56.242 27.181 1.00163.10 S ATOM 12297 SG CYS A 668 63.967 55.540 29.399 1.00132.88 S ATOM 12320 SG CYS A 671 65.726 58.563 30.102 1.00117.63 S ATOM 12748 SG CYS B 663 46.002 45.510 26.823 1.00165.19 S ATOM 12907 SG CYS B 683 45.232 42.621 24.456 1.00180.95 S ATOM 12927 SG CYS B 686 46.101 41.812 28.046 1.00190.72 S ATOM 12639 SG CYS B 648 46.524 47.106 15.051 1.00200.95 S ATOM 12659 SG CYS B 651 46.478 47.902 11.323 1.00193.03 S ATOM 12786 SG CYS B 668 44.323 50.001 13.668 1.00189.88 S ATOM 12809 SG CYS B 671 43.300 46.598 13.122 1.00200.12 S Time building chain proxies: 7.21, per 1000 atoms: 0.51 Number of scatterers: 14102 At special positions: 0 Unit cell: (120.288, 122.436, 111.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 41 16.00 P 294 15.00 O 3191 8.00 N 2632 7.00 C 7940 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: 6.86 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 665 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 683 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 663 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 686 " pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 668 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 671 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 648 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 651 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" ND1 HIS B 665 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 683 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 663 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 686 " pdb=" ZN B 802 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 671 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 668 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 651 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 648 " Number of angles added : 18 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 62.9% alpha, 5.3% beta 140 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 6.62 Creating SS restraints... Processing helix chain 'K' and resid 44 through 55 Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 131 removed outlier: 3.556A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.127A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.527A pdb=" N GLN L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.557A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.470A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.535A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.539A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.504A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.533A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.635A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.601A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.777A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.406A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'A' and resid 638 through 647 Processing helix chain 'A' and resid 668 through 678 Processing helix chain 'B' and resid 639 through 647 Processing helix chain 'B' and resid 668 through 678 Processing helix chain 'B' and resid 691 through 693 No H-bonds generated for 'chain 'B' and resid 691 through 693' Processing helix chain 'R' and resid 4 through 19 Processing helix chain 'R' and resid 89 through 94 Processing helix chain 'R' and resid 101 through 115 removed outlier: 3.736A pdb=" N ASN R 114 " --> pdb=" O GLN R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 133 Processing helix chain 'R' and resid 133 through 150 Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.873A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'L' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.296A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 removed outlier: 6.809A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.098A 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 42 through 43 removed outlier: 7.324A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'A' and resid 666 through 667 Processing sheet with id=AB3, first strand: chain 'B' and resid 666 through 667 Processing sheet with id=AB4, first strand: chain 'R' and resid 24 through 29 removed outlier: 3.636A pdb=" N MET R 39 " --> pdb=" O SER R 25 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER R 27 " --> pdb=" O ASN R 37 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL R 35 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU R 58 " --> pdb=" O HIS R 69 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS R 69 " --> pdb=" O GLU R 58 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 716 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 5.47 Time building geometry restraints manager: 7.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3261 1.34 - 1.45: 4336 1.45 - 1.57: 6714 1.57 - 1.69: 586 1.69 - 1.81: 60 Bond restraints: 14957 Sorted by residual: bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" CD GLU K 97 " pdb=" OE1 GLU K 97 " ideal model delta sigma weight residual 1.249 1.223 0.026 1.90e-02 2.77e+03 1.91e+00 bond pdb=" CG GLU K 97 " pdb=" CD GLU K 97 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.87e+00 bond pdb=" CG1 ILE F 50 " pdb=" CD1 ILE F 50 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.49e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.46e+00 ... (remaining 14952 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.08: 1884 106.08 - 113.05: 8011 113.05 - 120.02: 5678 120.02 - 126.99: 5164 126.99 - 133.96: 746 Bond angle restraints: 21483 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.53 108.09 5.44 9.80e-01 1.04e+00 3.08e+01 angle pdb=" N ARG R 7 " pdb=" CA ARG R 7 " pdb=" C ARG R 7 " ideal model delta sigma weight residual 111.14 106.25 4.89 1.08e+00 8.57e-01 2.05e+01 angle pdb=" N GLU K 97 " pdb=" CA GLU K 97 " pdb=" CB GLU K 97 " ideal model delta sigma weight residual 110.12 115.83 -5.71 1.47e+00 4.63e-01 1.51e+01 angle pdb=" N MET B 680 " pdb=" CA MET B 680 " pdb=" C MET B 680 " ideal model delta sigma weight residual 110.68 105.93 4.75 1.39e+00 5.18e-01 1.17e+01 angle pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 122.46 126.81 -4.35 1.41e+00 5.03e-01 9.53e+00 ... (remaining 21478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 6823 33.77 - 67.54: 1411 67.54 - 101.32: 13 101.32 - 135.09: 1 135.09 - 168.86: 3 Dihedral angle restraints: 8251 sinusoidal: 5234 harmonic: 3017 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 51.14 168.86 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 68.60 151.40 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA ILE L 29 " pdb=" C ILE L 29 " pdb=" N THR L 30 " pdb=" CA THR L 30 " ideal model delta harmonic sigma weight residual -180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 8248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1694 0.033 - 0.067: 595 0.067 - 0.100: 110 0.100 - 0.133: 44 0.133 - 0.166: 6 Chirality restraints: 2449 Sorted by residual: chirality pdb=" CA ILE L 29 " pdb=" N ILE L 29 " pdb=" C ILE L 29 " pdb=" CB ILE L 29 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA GLU K 97 " pdb=" N GLU K 97 " pdb=" C GLU K 97 " pdb=" CB GLU K 97 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 2446 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 92 " -0.192 9.50e-02 1.11e+02 8.63e-02 4.72e+00 pdb=" NE ARG F 92 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG F 92 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG F 92 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG F 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 63 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO R 64 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO R 64 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 64 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.24e+00 pdb=" N PRO D 103 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.021 5.00e-02 4.00e+02 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 35 2.35 - 2.99: 6288 2.99 - 3.63: 22643 3.63 - 4.26: 37950 4.26 - 4.90: 55040 Nonbonded interactions: 121956 Sorted by model distance: nonbonded pdb=" O HIS A 699 " pdb=" O LEU A 700 " model vdw 1.714 3.040 nonbonded pdb=" NH2 ARG B 679 " pdb=" CD ARG B 681 " model vdw 1.885 3.520 nonbonded pdb=" OD2 ASP C 90 " pdb=" NH2 ARG A 679 " model vdw 1.941 2.520 nonbonded pdb=" CD2 LEU C 65 " pdb=" NH1 ARG A 681 " model vdw 1.965 3.540 nonbonded pdb=" CB PRO R 4 " pdb=" NH1 ARG R 7 " model vdw 2.088 3.520 ... (remaining 121951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 638 through 652 or (resid 653 and (name N or name CA or na \ me C or name O or name CB )) or resid 654 through 660 or (resid 661 and (name N \ or name CA or name C or name O or name CB )) or resid 662 through 700 or resid 8 \ 01 through 802)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 119 or resid 121 through 124)) selection = (chain 'H' and (resid 31 through 119 or resid 121 through 124)) } ncs_group { reference = chain 'E' selection = (chain 'K' and resid 38 through 134) } ncs_group { reference = chain 'F' selection = (chain 'L' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) } 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: 0.790 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: 4.200 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 47.280 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 : 0.004 0.048 14957 Z= 0.199 Angle : 0.604 7.993 21483 Z= 0.385 Chirality : 0.036 0.166 2449 Planarity : 0.005 0.086 1707 Dihedral : 25.787 168.858 6293 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.43 % Allowed : 1.78 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.84 (0.27), residues: 1013 helix: 1.36 (0.21), residues: 639 sheet: -1.45 (0.86), residues: 41 loop : -0.66 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 96 HIS 0.003 0.001 HIS C 82 PHE 0.016 0.002 PHE B 642 TYR 0.018 0.001 TYR D 40 ARG 0.007 0.001 ARG L 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 393 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 49 LEU cc_start: 0.8407 (mt) cc_final: 0.7814 (mm) REVERT: C 39 TYR cc_start: 0.7556 (m-80) cc_final: 0.7050 (m-80) REVERT: C 57 TYR cc_start: 0.8657 (t80) cc_final: 0.8428 (t80) REVERT: C 61 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7300 (tp30) REVERT: C 94 ASN cc_start: 0.8311 (t0) cc_final: 0.8079 (t0) REVERT: D 92 ARG cc_start: 0.7481 (ttt90) cc_final: 0.7249 (ttt90) REVERT: A 642 PHE cc_start: 0.3287 (m-10) cc_final: 0.3073 (m-10) REVERT: A 662 THR cc_start: 0.7869 (m) cc_final: 0.7514 (t) REVERT: A 669 GLU cc_start: 0.7203 (pp20) cc_final: 0.6833 (tm-30) REVERT: B 647 TYR cc_start: 0.2572 (m-80) cc_final: 0.2233 (m-80) REVERT: B 679 ARG cc_start: 0.2542 (OUTLIER) cc_final: 0.1385 (tpt90) REVERT: R 81 VAL cc_start: 0.7850 (t) cc_final: 0.7331 (t) REVERT: R 82 TYR cc_start: 0.8261 (m-80) cc_final: 0.7880 (m-80) REVERT: R 90 ASP cc_start: 0.8777 (p0) cc_final: 0.8479 (p0) REVERT: R 110 GLN cc_start: 0.2991 (OUTLIER) cc_final: 0.2362 (tt0) outliers start: 12 outliers final: 2 residues processed: 398 average time/residue: 0.3320 time to fit residues: 175.9785 Evaluate side-chains 271 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 267 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 679 ARG Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 110 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 32 optimal weight: 0.0270 chunk 63 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 113 HIS C 73 ASN D 49 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 104 GLN A 699 HIS ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14957 Z= 0.235 Angle : 0.589 7.215 21483 Z= 0.347 Chirality : 0.036 0.149 2449 Planarity : 0.004 0.039 1707 Dihedral : 29.139 170.755 4362 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.38 % Allowed : 14.86 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.31 (0.27), residues: 1013 helix: 1.73 (0.21), residues: 649 sheet: -1.53 (0.73), residues: 50 loop : -0.48 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP R 149 HIS 0.004 0.001 HIS C 31 PHE 0.021 0.002 PHE R 72 TYR 0.017 0.002 TYR D 40 ARG 0.010 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 272 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 108 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7841 (ttmm) REVERT: E 79 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7631 (tttt) REVERT: F 77 LYS cc_start: 0.8761 (mttt) cc_final: 0.8555 (mttp) REVERT: H 33 ARG cc_start: 0.4738 (mtp85) cc_final: 0.4349 (ttm170) REVERT: H 83 TYR cc_start: 0.6990 (m-10) cc_final: 0.6705 (m-80) REVERT: A 669 GLU cc_start: 0.7316 (pp20) cc_final: 0.6970 (tm-30) REVERT: A 673 LYS cc_start: 0.8986 (pttt) cc_final: 0.8745 (pttp) REVERT: R 8 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7096 (tpt-90) REVERT: R 90 ASP cc_start: 0.8561 (p0) cc_final: 0.8267 (p0) REVERT: R 110 GLN cc_start: 0.2207 (OUTLIER) cc_final: 0.1927 (tp40) outliers start: 20 outliers final: 10 residues processed: 284 average time/residue: 0.2861 time to fit residues: 113.1318 Evaluate side-chains 261 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 248 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 122 optimal weight: 30.0000 chunk 101 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN G 73 ASN G 104 GLN A 699 HIS ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14957 Z= 0.362 Angle : 0.640 9.375 21483 Z= 0.370 Chirality : 0.039 0.142 2449 Planarity : 0.005 0.055 1707 Dihedral : 29.782 171.815 4356 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.28 % Allowed : 17.12 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.27), residues: 1013 helix: 1.74 (0.20), residues: 650 sheet: -1.03 (0.75), residues: 47 loop : -0.60 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP R 149 HIS 0.008 0.002 HIS R 133 PHE 0.031 0.002 PHE R 72 TYR 0.020 0.002 TYR G 39 ARG 0.004 0.001 ARG K 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 260 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ASN cc_start: 0.8461 (t0) cc_final: 0.8251 (t0) REVERT: E 79 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7761 (tttt) REVERT: F 77 LYS cc_start: 0.8845 (mttt) cc_final: 0.8643 (mttp) REVERT: F 88 TYR cc_start: 0.8350 (m-10) cc_final: 0.8032 (m-80) REVERT: H 83 TYR cc_start: 0.7125 (m-10) cc_final: 0.6157 (m-10) REVERT: A 667 PHE cc_start: 0.7956 (m-80) cc_final: 0.7544 (m-80) REVERT: A 669 GLU cc_start: 0.7494 (pp20) cc_final: 0.7119 (tm-30) REVERT: B 680 MET cc_start: 0.6195 (tpp) cc_final: 0.5949 (ptp) REVERT: R 40 ILE cc_start: 0.6414 (mt) cc_final: 0.6188 (mt) REVERT: R 90 ASP cc_start: 0.8479 (p0) cc_final: 0.8137 (p0) outliers start: 36 outliers final: 19 residues processed: 275 average time/residue: 0.2819 time to fit residues: 108.9844 Evaluate side-chains 261 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 241 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 110 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 120 optimal weight: 0.0870 chunk 108 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14957 Z= 0.185 Angle : 0.577 7.887 21483 Z= 0.336 Chirality : 0.035 0.144 2449 Planarity : 0.004 0.037 1707 Dihedral : 29.392 170.241 4352 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.45 % Allowed : 19.74 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.27), residues: 1013 helix: 1.95 (0.21), residues: 650 sheet: -0.79 (0.74), residues: 48 loop : -0.56 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 149 HIS 0.005 0.001 HIS R 78 PHE 0.023 0.002 PHE R 72 TYR 0.014 0.001 TYR C 39 ARG 0.003 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 264 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 88 TYR cc_start: 0.8198 (m-10) cc_final: 0.7953 (m-10) REVERT: F 92 ARG cc_start: 0.8040 (tpt-90) cc_final: 0.7809 (ttt90) REVERT: A 667 PHE cc_start: 0.7826 (m-80) cc_final: 0.7395 (m-80) REVERT: A 669 GLU cc_start: 0.7379 (pp20) cc_final: 0.7055 (tm-30) REVERT: A 673 LYS cc_start: 0.8747 (pttt) cc_final: 0.8376 (pttp) REVERT: B 695 LEU cc_start: 0.6925 (tt) cc_final: 0.6407 (mp) REVERT: R 89 LEU cc_start: 0.8230 (tp) cc_final: 0.7802 (pt) REVERT: R 90 ASP cc_start: 0.8241 (p0) cc_final: 0.7743 (p0) REVERT: R 110 GLN cc_start: 0.2592 (OUTLIER) cc_final: 0.2367 (mm110) outliers start: 29 outliers final: 16 residues processed: 277 average time/residue: 0.2762 time to fit residues: 107.5719 Evaluate side-chains 263 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 246 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 110 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14957 Z= 0.259 Angle : 0.600 8.718 21483 Z= 0.348 Chirality : 0.036 0.154 2449 Planarity : 0.004 0.037 1707 Dihedral : 29.547 170.253 4352 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.04 % Allowed : 20.93 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.60 (0.27), residues: 1013 helix: 1.99 (0.20), residues: 649 sheet: -0.47 (0.78), residues: 47 loop : -0.65 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP R 149 HIS 0.013 0.001 HIS R 133 PHE 0.020 0.002 PHE R 72 TYR 0.030 0.002 TYR H 83 ARG 0.010 0.001 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 245 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLU cc_start: 0.7929 (tp30) cc_final: 0.7719 (tp30) REVERT: A 669 GLU cc_start: 0.7474 (pp20) cc_final: 0.6104 (tm-30) REVERT: A 673 LYS cc_start: 0.8756 (pttt) cc_final: 0.8084 (pttt) REVERT: B 680 MET cc_start: 0.5786 (tpp) cc_final: 0.5213 (ptp) REVERT: B 695 LEU cc_start: 0.6709 (tt) cc_final: 0.6166 (mt) outliers start: 34 outliers final: 20 residues processed: 262 average time/residue: 0.2695 time to fit residues: 99.8926 Evaluate side-chains 258 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 238 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 110 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 120 optimal weight: 0.0870 chunk 100 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 76 GLN E 76 GLN ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14957 Z= 0.205 Angle : 0.586 9.976 21483 Z= 0.339 Chirality : 0.035 0.160 2449 Planarity : 0.004 0.045 1707 Dihedral : 29.361 169.235 4352 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.26 % Allowed : 23.07 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.27), residues: 1013 helix: 2.08 (0.21), residues: 649 sheet: -0.22 (0.79), residues: 47 loop : -0.56 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP R 149 HIS 0.005 0.001 HIS R 78 PHE 0.014 0.001 PHE R 13 TYR 0.015 0.001 TYR C 39 ARG 0.011 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 250 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLU cc_start: 0.7892 (tp30) cc_final: 0.7692 (tp30) REVERT: A 667 PHE cc_start: 0.7577 (m-80) cc_final: 0.7183 (m-80) REVERT: A 669 GLU cc_start: 0.7534 (pp20) cc_final: 0.7285 (tm-30) REVERT: A 673 LYS cc_start: 0.8827 (pttt) cc_final: 0.8538 (pttp) REVERT: B 680 MET cc_start: 0.5852 (tpp) cc_final: 0.5418 (ptp) outliers start: 19 outliers final: 14 residues processed: 260 average time/residue: 0.2756 time to fit residues: 102.5635 Evaluate side-chains 251 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 237 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 110 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 101 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 76 GLN ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14957 Z= 0.189 Angle : 0.601 10.670 21483 Z= 0.343 Chirality : 0.035 0.156 2449 Planarity : 0.004 0.054 1707 Dihedral : 29.267 168.904 4352 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.38 % Allowed : 24.85 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.27), residues: 1013 helix: 2.07 (0.21), residues: 649 sheet: -0.23 (0.78), residues: 47 loop : -0.51 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP R 149 HIS 0.004 0.001 HIS R 78 PHE 0.024 0.002 PHE R 13 TYR 0.026 0.002 TYR R 137 ARG 0.012 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 255 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 GLU cc_start: 0.7867 (tp30) cc_final: 0.7647 (tp30) REVERT: A 658 MET cc_start: 0.6584 (tpp) cc_final: 0.6367 (tpp) REVERT: A 669 GLU cc_start: 0.7638 (pp20) cc_final: 0.7098 (tm-30) REVERT: A 673 LYS cc_start: 0.8875 (pttt) cc_final: 0.8440 (pttp) REVERT: B 695 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6466 (mt) REVERT: R 129 LEU cc_start: 0.4615 (tp) cc_final: 0.4072 (mt) outliers start: 20 outliers final: 15 residues processed: 263 average time/residue: 0.2653 time to fit residues: 99.9364 Evaluate side-chains 261 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 245 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 102 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 115 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14957 Z= 0.342 Angle : 0.663 9.799 21483 Z= 0.377 Chirality : 0.039 0.174 2449 Planarity : 0.005 0.061 1707 Dihedral : 29.786 169.363 4349 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.80 % Allowed : 23.42 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.49 (0.27), residues: 1013 helix: 1.90 (0.21), residues: 648 sheet: -0.67 (0.73), residues: 49 loop : -0.64 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP R 36 HIS 0.024 0.002 HIS R 133 PHE 0.029 0.002 PHE R 13 TYR 0.025 0.002 TYR R 137 ARG 0.013 0.001 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 240 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.6358 (pp20) cc_final: 0.6074 (pp20) REVERT: D 76 GLU cc_start: 0.7941 (tp30) cc_final: 0.7720 (tp30) REVERT: D 95 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7794 (tp40) REVERT: A 667 PHE cc_start: 0.8080 (m-80) cc_final: 0.7724 (m-80) REVERT: A 669 GLU cc_start: 0.7760 (pp20) cc_final: 0.7037 (tm-30) REVERT: A 673 LYS cc_start: 0.8851 (pttt) cc_final: 0.8324 (pttm) REVERT: A 682 LYS cc_start: 0.8039 (mmmt) cc_final: 0.7792 (mmmt) REVERT: R 129 LEU cc_start: 0.5133 (tp) cc_final: 0.4200 (mt) outliers start: 32 outliers final: 22 residues processed: 257 average time/residue: 0.2853 time to fit residues: 104.3246 Evaluate side-chains 259 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 236 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 133 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 118 optimal weight: 0.0070 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 76 GLN E 93 GLN A 670 ASN ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14957 Z= 0.194 Angle : 0.634 11.056 21483 Z= 0.355 Chirality : 0.035 0.164 2449 Planarity : 0.004 0.058 1707 Dihedral : 29.318 167.614 4349 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.38 % Allowed : 25.45 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.27), residues: 1013 helix: 2.04 (0.21), residues: 648 sheet: -0.67 (0.73), residues: 49 loop : -0.61 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP R 149 HIS 0.021 0.001 HIS R 133 PHE 0.017 0.002 PHE R 13 TYR 0.018 0.001 TYR G 57 ARG 0.014 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 262 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 667 PHE cc_start: 0.7914 (m-80) cc_final: 0.7609 (m-80) REVERT: R 129 LEU cc_start: 0.4519 (tp) cc_final: 0.3791 (mt) outliers start: 20 outliers final: 15 residues processed: 269 average time/residue: 0.2852 time to fit residues: 109.1400 Evaluate side-chains 264 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 249 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 133 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 10 optimal weight: 0.0970 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 76 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 14957 Z= 0.383 Angle : 0.701 10.436 21483 Z= 0.393 Chirality : 0.040 0.168 2449 Planarity : 0.005 0.076 1707 Dihedral : 29.815 168.599 4349 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.38 % Allowed : 26.52 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.35 (0.27), residues: 1013 helix: 1.85 (0.21), residues: 648 sheet: -0.85 (0.76), residues: 49 loop : -0.82 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP R 36 HIS 0.019 0.002 HIS R 133 PHE 0.027 0.002 PHE R 13 TYR 0.038 0.002 TYR G 57 ARG 0.006 0.001 ARG A 679 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 234 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 GLU cc_start: 0.6014 (tm-30) cc_final: 0.5405 (mm-30) REVERT: A 674 GLU cc_start: 0.8565 (pp20) cc_final: 0.8197 (pp20) REVERT: R 106 LEU cc_start: 0.8802 (mt) cc_final: 0.8580 (pp) REVERT: R 129 LEU cc_start: 0.4905 (tp) cc_final: 0.4026 (mt) outliers start: 20 outliers final: 16 residues processed: 242 average time/residue: 0.2641 time to fit residues: 90.8520 Evaluate side-chains 248 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 133 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 14 optimal weight: 0.0370 chunk 27 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 87 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 75 HIS ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.067746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.045501 restraints weight = 66256.575| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.36 r_work: 0.2756 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14957 Z= 0.186 Angle : 0.648 11.468 21483 Z= 0.361 Chirality : 0.036 0.161 2449 Planarity : 0.004 0.053 1707 Dihedral : 29.262 166.739 4349 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.90 % Allowed : 26.87 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.50 (0.27), residues: 1013 helix: 2.00 (0.21), residues: 647 sheet: -1.19 (0.70), residues: 49 loop : -0.74 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP R 149 HIS 0.022 0.001 HIS R 133 PHE 0.016 0.002 PHE R 13 TYR 0.032 0.002 TYR G 57 ARG 0.005 0.000 ARG A 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3095.22 seconds wall clock time: 56 minutes 1.63 seconds (3361.63 seconds total)