Starting phenix.real_space_refine on Sun Nov 17 17:45:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7j_38100/11_2024/8x7j_38100.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7j_38100/11_2024/8x7j_38100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7j_38100/11_2024/8x7j_38100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7j_38100/11_2024/8x7j_38100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7j_38100/11_2024/8x7j_38100.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7j_38100/11_2024/8x7j_38100.cif" } resolution = 3.39 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 Anisotropic ADP refinement not supported. Converting 1025 atoms to isotropic. 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 2 6.06 5 P 288 5.49 5 S 25 5.16 5 C 7736 2.51 5 N 2547 2.21 5 O 3141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13739 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 642 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} 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: "C" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} 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: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2967 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2937 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "K" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1031 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 126} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "L" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 405 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 399 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 56} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "L" 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 13064 SG CYS L 31 59.328 67.509 25.982 1.00218.04 S ATOM 13203 SG CYS L 51 60.840 71.001 26.041 1.00210.14 S ATOM 13227 SG CYS L 54 57.120 70.534 25.078 1.00213.50 S ATOM 12959 SG CYS L 16 71.165 67.606 21.224 1.00283.03 S ATOM 12977 SG CYS L 19 74.736 68.117 20.046 1.00282.47 S ATOM 13100 SG CYS L 36 74.096 65.680 22.767 1.00253.66 S ATOM 13118 SG CYS L 39 73.702 69.387 23.482 1.00248.31 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 75 " occ=0.45 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.45 Time building chain proxies: 8.80, per 1000 atoms: 0.64 Number of scatterers: 13739 At special positions: 0 Unit cell: (118.14, 125.658, 112.77, 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 2 29.99 S 25 16.00 P 288 15.00 O 3141 8.00 N 2547 7.00 C 7736 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 - 3.00 Amino acid : True - 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: 3.43 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 33 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 54 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 16 " Number of angles added : 9 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1918 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 13 sheets defined 63.1% alpha, 4.4% beta 143 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 6.85 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.515A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.870A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.472A 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 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.310A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.522A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 29 removed outlier: 4.026A pdb=" N ASN F 25 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.886A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.730A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.526A 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 104 through 124 Processing helix chain 'K' and resid 3 through 16 Processing helix chain 'K' and resid 86 through 91 Processing helix chain 'K' and resid 98 through 112 Processing helix chain 'K' and resid 120 through 130 Processing helix chain 'K' and resid 130 through 145 Processing helix chain 'L' and resid 36 through 44 Processing helix chain 'L' and resid 58 through 67 removed outlier: 3.859A pdb=" N ARG L 67 " --> pdb=" O ARG L 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.965A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.940A 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 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.911A 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: 7.307A 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 'K' and resid 32 through 38 Processing sheet with id=AB3, first strand: chain 'L' and resid 27 through 28 Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 6 removed outlier: 5.969A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 478 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 5.20 Time building geometry restraints manager: 3.99 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: 3179 1.34 - 1.45: 4115 1.45 - 1.57: 6668 1.57 - 1.69: 574 1.69 - 1.81: 38 Bond restraints: 14574 Sorted by residual: bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" N PRO M 37 " pdb=" CA PRO M 37 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.31e-02 5.83e+03 8.73e-01 bond pdb=" C3' DG I 21 " pdb=" C2' DG I 21 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 8.70e-01 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 8.22e-01 ... (remaining 14569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 19803 1.04 - 2.08: 911 2.08 - 3.13: 225 3.13 - 4.17: 16 4.17 - 5.21: 9 Bond angle restraints: 20964 Sorted by residual: angle pdb=" C VAL M 17 " pdb=" N GLU M 18 " pdb=" CA GLU M 18 " ideal model delta sigma weight residual 121.03 125.12 -4.09 1.60e+00 3.91e-01 6.55e+00 angle pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" C2' DT I -59 " ideal model delta sigma weight residual 102.40 105.59 -3.19 1.50e+00 4.44e-01 4.51e+00 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 123.36 -3.16 1.50e+00 4.44e-01 4.43e+00 angle pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sigma weight residual 120.20 123.23 -3.03 1.50e+00 4.44e-01 4.08e+00 angle pdb=" C3' DA J -44 " pdb=" C2' DA J -44 " pdb=" C1' DA J -44 " ideal model delta sigma weight residual 101.60 104.53 -2.93 1.50e+00 4.44e-01 3.83e+00 ... (remaining 20959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 6717 35.75 - 71.50: 1268 71.50 - 107.25: 20 107.25 - 143.01: 1 143.01 - 178.76: 2 Dihedral angle restraints: 8008 sinusoidal: 5051 harmonic: 2957 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 -140.00 38.76 -178.76 1 3.50e+01 8.16e-04 1.57e+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 53.55 166.45 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 83.64 136.36 1 3.50e+01 8.16e-04 1.35e+01 ... (remaining 8005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1551 0.026 - 0.053: 603 0.053 - 0.079: 166 0.079 - 0.105: 66 0.105 - 0.131: 24 Chirality restraints: 2410 Sorted by residual: chirality pdb=" CA ILE M 36 " pdb=" N ILE M 36 " pdb=" C ILE M 36 " pdb=" CB ILE M 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE K 73 " pdb=" N ILE K 73 " pdb=" C ILE K 73 " pdb=" CB ILE K 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 2407 not shown) Planarity restraints: 1663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 48 " 0.020 2.00e-02 2.50e+03 8.19e-03 2.01e+00 pdb=" N9 DG I 48 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DG I 48 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 48 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 48 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 48 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 48 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 48 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 48 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 48 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 48 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 48 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO H 103 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 8 " -0.017 2.00e-02 2.50e+03 7.87e-03 1.86e+00 pdb=" N9 DG I 8 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DG I 8 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 8 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 8 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 8 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 8 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DG I 8 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 8 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG I 8 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG I 8 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 8 " 0.002 2.00e-02 2.50e+03 ... (remaining 1660 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 104 2.49 - 3.09: 9046 3.09 - 3.69: 24450 3.69 - 4.30: 34292 4.30 - 4.90: 50522 Nonbonded interactions: 118414 Sorted by model distance: nonbonded pdb=" SG CYS L 54 " pdb=" CD ARG L 56 " model vdw 1.882 3.800 nonbonded pdb=" N2 DG I 56 " pdb=" O2 DC J -56 " model vdw 2.048 2.496 nonbonded pdb=" N2 DG I -42 " pdb=" O2 DC J 42 " model vdw 2.069 2.496 nonbonded pdb=" O2 DC I 52 " pdb=" N2 DG J -52 " model vdw 2.082 2.496 nonbonded pdb=" N2 DG I 21 " pdb=" O2 DC J -21 " model vdw 2.095 2.496 ... (remaining 118409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = (chain 'C' and (resid 11 through 14 or resid 16 through 117)) selection = (chain 'G' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 117)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 123) } 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=0.00 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.140 Find NCS groups from input model: 0.330 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 0.003 0.040 14574 Z= 0.174 Angle : 0.516 5.210 20964 Z= 0.317 Chirality : 0.033 0.131 2410 Planarity : 0.003 0.034 1663 Dihedral : 25.848 178.758 6090 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.73 % Allowed : 4.46 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % 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: 2.58 (0.28), residues: 988 helix: 2.81 (0.21), residues: 636 sheet: -0.95 (0.96), residues: 28 loop : -0.35 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 93 HIS 0.002 0.001 HIS M 68 PHE 0.008 0.001 PHE E 67 TYR 0.008 0.001 TYR F 72 ARG 0.002 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 253 time to evaluate : 1.345 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: B 49 LEU cc_start: 0.9256 (mt) cc_final: 0.8300 (mp) REVERT: C 56 GLU cc_start: 0.8368 (tt0) cc_final: 0.8107 (tt0) REVERT: C 68 ASN cc_start: 0.8931 (m-40) cc_final: 0.7374 (m-40) REVERT: D 68 ASP cc_start: 0.8713 (t70) cc_final: 0.8399 (t0) REVERT: E 73 GLU cc_start: 0.7680 (tt0) cc_final: 0.7463 (tt0) REVERT: E 94 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8133 (mm-30) REVERT: G 56 GLU cc_start: 0.8579 (tt0) cc_final: 0.8331 (tt0) REVERT: G 68 ASN cc_start: 0.8179 (m-40) cc_final: 0.7725 (m-40) REVERT: H 62 MET cc_start: 0.9329 (mmm) cc_final: 0.8971 (mmt) REVERT: H 68 ASP cc_start: 0.8817 (t70) cc_final: 0.8576 (t0) REVERT: K 92 GLN cc_start: 0.9289 (tp-100) cc_final: 0.8958 (tp-100) REVERT: K 147 MET cc_start: 0.7873 (mtt) cc_final: 0.7045 (mtt) outliers start: 14 outliers final: 8 residues processed: 263 average time/residue: 0.3281 time to fit residues: 115.8960 Evaluate side-chains 187 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 56 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 63 optimal weight: 0.0030 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 64 ASN B 75 HIS D 47 GLN D 109 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14574 Z= 0.178 Angle : 0.565 9.156 20964 Z= 0.331 Chirality : 0.035 0.148 2410 Planarity : 0.004 0.034 1663 Dihedral : 29.675 178.942 4274 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.23 % Allowed : 11.77 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % 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: 2.47 (0.27), residues: 988 helix: 2.70 (0.21), residues: 642 sheet: -0.42 (1.05), residues: 28 loop : -0.45 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 141 HIS 0.002 0.001 HIS D 109 PHE 0.008 0.001 PHE A 67 TYR 0.028 0.002 TYR D 83 ARG 0.008 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9093 (mt) cc_final: 0.8751 (mp) REVERT: B 88 TYR cc_start: 0.8925 (m-10) cc_final: 0.8266 (m-10) REVERT: C 56 GLU cc_start: 0.8400 (tt0) cc_final: 0.8151 (tt0) REVERT: C 68 ASN cc_start: 0.8601 (m-40) cc_final: 0.8317 (m-40) REVERT: D 51 ASP cc_start: 0.8355 (p0) cc_final: 0.8138 (p0) REVERT: D 67 ASN cc_start: 0.9081 (m-40) cc_final: 0.8821 (m-40) REVERT: D 68 ASP cc_start: 0.8751 (t70) cc_final: 0.8459 (t0) REVERT: E 94 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8131 (mt-10) REVERT: G 38 ASN cc_start: 0.7046 (t0) cc_final: 0.6618 (t0) REVERT: G 56 GLU cc_start: 0.8578 (tt0) cc_final: 0.8327 (tt0) REVERT: H 68 ASP cc_start: 0.8830 (t70) cc_final: 0.8570 (t0) REVERT: H 79 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7739 (mtm-85) REVERT: H 113 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8562 (mt-10) REVERT: K 147 MET cc_start: 0.7864 (mtt) cc_final: 0.7008 (mtt) REVERT: L 42 SER cc_start: 0.8257 (m) cc_final: 0.7895 (p) REVERT: M 1 MET cc_start: 0.7617 (ptt) cc_final: 0.6497 (ppp) outliers start: 18 outliers final: 13 residues processed: 205 average time/residue: 0.2840 time to fit residues: 82.0509 Evaluate side-chains 186 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 122 optimal weight: 0.0170 chunk 101 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 64 ASN D 82 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 14574 Z= 0.345 Angle : 0.611 9.222 20964 Z= 0.357 Chirality : 0.038 0.155 2410 Planarity : 0.004 0.046 1663 Dihedral : 29.766 177.440 4262 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.60 % Allowed : 12.64 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % 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: 2.34 (0.27), residues: 988 helix: 2.54 (0.21), residues: 642 sheet: 0.21 (1.17), residues: 23 loop : -0.43 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 93 HIS 0.004 0.001 HIS M 68 PHE 0.011 0.001 PHE C 25 TYR 0.028 0.002 TYR D 83 ARG 0.004 0.001 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8460 (tt0) cc_final: 0.8203 (tt0) REVERT: C 64 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8226 (tm-30) REVERT: C 65 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9337 (mm) REVERT: C 68 ASN cc_start: 0.8631 (m-40) cc_final: 0.8224 (m-40) REVERT: D 68 ASP cc_start: 0.8955 (t70) cc_final: 0.8676 (t0) REVERT: F 22 LEU cc_start: 0.7855 (pt) cc_final: 0.7534 (tt) REVERT: G 38 ASN cc_start: 0.7398 (t0) cc_final: 0.7008 (t0) REVERT: G 56 GLU cc_start: 0.8591 (tt0) cc_final: 0.8299 (tt0) REVERT: H 68 ASP cc_start: 0.8890 (t70) cc_final: 0.8637 (t0) REVERT: K 89 LEU cc_start: 0.9040 (mt) cc_final: 0.8806 (tp) REVERT: K 147 MET cc_start: 0.7574 (mtt) cc_final: 0.6628 (mtt) REVERT: L 42 SER cc_start: 0.7944 (m) cc_final: 0.7643 (p) REVERT: M 1 MET cc_start: 0.7770 (ptt) cc_final: 0.6429 (mtp) outliers start: 21 outliers final: 16 residues processed: 186 average time/residue: 0.2730 time to fit residues: 72.9743 Evaluate side-chains 176 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 0.0970 chunk 120 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN H 109 HIS K 7 ASN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14574 Z= 0.220 Angle : 0.568 9.171 20964 Z= 0.337 Chirality : 0.035 0.148 2410 Planarity : 0.004 0.054 1663 Dihedral : 29.715 178.141 4262 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.60 % Allowed : 13.88 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % 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: 2.37 (0.28), residues: 988 helix: 2.60 (0.21), residues: 643 sheet: -0.60 (1.02), residues: 28 loop : -0.42 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 141 HIS 0.002 0.001 HIS M 68 PHE 0.010 0.001 PHE E 67 TYR 0.020 0.001 TYR D 83 ARG 0.006 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8394 (tt0) cc_final: 0.8156 (tt0) REVERT: C 64 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8159 (tm-30) REVERT: C 65 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9268 (mm) REVERT: C 68 ASN cc_start: 0.8606 (m-40) cc_final: 0.8111 (m-40) REVERT: D 63 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8600 (m-40) REVERT: D 68 ASP cc_start: 0.8873 (t70) cc_final: 0.8592 (t0) REVERT: E 94 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7988 (mt-10) REVERT: F 22 LEU cc_start: 0.7917 (pt) cc_final: 0.7635 (tt) REVERT: G 38 ASN cc_start: 0.7297 (t0) cc_final: 0.7035 (t0) REVERT: G 56 GLU cc_start: 0.8531 (tt0) cc_final: 0.8283 (tt0) REVERT: G 89 ASN cc_start: 0.8907 (m-40) cc_final: 0.8639 (m-40) REVERT: H 37 TYR cc_start: 0.8738 (m-80) cc_final: 0.8422 (m-80) REVERT: H 68 ASP cc_start: 0.8860 (t70) cc_final: 0.8634 (t0) REVERT: H 79 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7846 (mtm-85) REVERT: K 89 LEU cc_start: 0.8976 (mt) cc_final: 0.8735 (tp) REVERT: K 147 MET cc_start: 0.7599 (mtt) cc_final: 0.6732 (mtt) REVERT: L 42 SER cc_start: 0.7954 (m) cc_final: 0.7649 (p) REVERT: M 1 MET cc_start: 0.6858 (ptt) cc_final: 0.6173 (mtp) outliers start: 21 outliers final: 15 residues processed: 187 average time/residue: 0.2822 time to fit residues: 76.0344 Evaluate side-chains 182 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14574 Z= 0.319 Angle : 0.598 8.536 20964 Z= 0.352 Chirality : 0.037 0.173 2410 Planarity : 0.004 0.055 1663 Dihedral : 29.739 177.558 4261 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.85 % Allowed : 15.24 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % 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: 2.19 (0.28), residues: 988 helix: 2.47 (0.21), residues: 643 sheet: -0.77 (1.02), residues: 28 loop : -0.52 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 33 HIS 0.004 0.001 HIS M 68 PHE 0.011 0.001 PHE E 67 TYR 0.017 0.001 TYR F 88 ARG 0.013 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8444 (tt0) cc_final: 0.8200 (tt0) REVERT: C 64 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8222 (tm-30) REVERT: C 65 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9362 (mm) REVERT: D 63 ASN cc_start: 0.9277 (OUTLIER) cc_final: 0.8658 (m-40) REVERT: D 68 ASP cc_start: 0.8922 (t70) cc_final: 0.8650 (t0) REVERT: E 94 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8002 (mt-10) REVERT: F 22 LEU cc_start: 0.7970 (pt) cc_final: 0.7704 (tt) REVERT: G 56 GLU cc_start: 0.8593 (tt0) cc_final: 0.8306 (tt0) REVERT: H 37 TYR cc_start: 0.8790 (m-80) cc_final: 0.8501 (m-80) REVERT: H 68 ASP cc_start: 0.8938 (t70) cc_final: 0.8717 (t0) REVERT: K 89 LEU cc_start: 0.8983 (mt) cc_final: 0.8733 (tp) REVERT: K 147 MET cc_start: 0.7468 (mtt) cc_final: 0.6591 (mtt) REVERT: L 20 MET cc_start: 0.7323 (mmt) cc_final: 0.6910 (mpp) REVERT: L 42 SER cc_start: 0.8004 (m) cc_final: 0.7727 (p) REVERT: M 1 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6475 (mtp) outliers start: 23 outliers final: 16 residues processed: 175 average time/residue: 0.2587 time to fit residues: 65.7035 Evaluate side-chains 177 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 116 optimal weight: 30.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14574 Z= 0.227 Angle : 0.575 8.007 20964 Z= 0.339 Chirality : 0.035 0.162 2410 Planarity : 0.004 0.055 1663 Dihedral : 29.687 177.943 4261 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.48 % Allowed : 16.60 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % 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: 2.24 (0.28), residues: 988 helix: 2.54 (0.21), residues: 643 sheet: -0.82 (1.00), residues: 28 loop : -0.57 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 33 HIS 0.002 0.001 HIS M 68 PHE 0.010 0.001 PHE E 67 TYR 0.014 0.001 TYR F 88 ARG 0.006 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8403 (tt0) cc_final: 0.8173 (tt0) REVERT: C 64 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8221 (tm-30) REVERT: C 65 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9320 (mm) REVERT: D 63 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8557 (m-40) REVERT: D 68 ASP cc_start: 0.8897 (t70) cc_final: 0.8632 (t0) REVERT: E 94 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8054 (mt-10) REVERT: F 22 LEU cc_start: 0.7920 (pt) cc_final: 0.7653 (tt) REVERT: G 56 GLU cc_start: 0.8570 (tt0) cc_final: 0.8295 (tt0) REVERT: G 89 ASN cc_start: 0.8905 (m-40) cc_final: 0.8641 (m-40) REVERT: H 37 TYR cc_start: 0.8800 (m-80) cc_final: 0.8515 (m-80) REVERT: H 79 ARG cc_start: 0.8431 (ttm110) cc_final: 0.7987 (ttm110) REVERT: K 89 LEU cc_start: 0.8979 (mt) cc_final: 0.8727 (tp) REVERT: K 147 MET cc_start: 0.7502 (mtt) cc_final: 0.6637 (mtt) REVERT: L 20 MET cc_start: 0.7311 (mmt) cc_final: 0.6875 (mpp) REVERT: L 42 SER cc_start: 0.8019 (m) cc_final: 0.7737 (p) outliers start: 20 outliers final: 15 residues processed: 186 average time/residue: 0.2594 time to fit residues: 70.1765 Evaluate side-chains 182 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14574 Z= 0.312 Angle : 0.600 7.610 20964 Z= 0.352 Chirality : 0.037 0.152 2410 Planarity : 0.004 0.066 1663 Dihedral : 29.722 177.071 4261 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.23 % Allowed : 17.22 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % 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: 2.11 (0.28), residues: 988 helix: 2.45 (0.21), residues: 643 sheet: -0.82 (1.01), residues: 28 loop : -0.64 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 33 HIS 0.003 0.001 HIS M 68 PHE 0.011 0.001 PHE E 67 TYR 0.045 0.002 TYR D 83 ARG 0.008 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8443 (tt0) cc_final: 0.8198 (tt0) REVERT: C 64 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8238 (tm-30) REVERT: C 65 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9285 (mm) REVERT: C 95 LYS cc_start: 0.9154 (tptt) cc_final: 0.8777 (tppt) REVERT: D 63 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.8599 (m-40) REVERT: D 68 ASP cc_start: 0.8934 (t70) cc_final: 0.8673 (t0) REVERT: F 22 LEU cc_start: 0.7957 (pt) cc_final: 0.7675 (tt) REVERT: G 56 GLU cc_start: 0.8593 (tt0) cc_final: 0.8284 (tt0) REVERT: G 89 ASN cc_start: 0.8885 (m-40) cc_final: 0.8622 (m-40) REVERT: H 37 TYR cc_start: 0.8830 (m-80) cc_final: 0.8551 (m-80) REVERT: H 76 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8178 (mm-30) REVERT: H 79 ARG cc_start: 0.8386 (ttm110) cc_final: 0.7905 (ttm110) REVERT: K 89 LEU cc_start: 0.8976 (mt) cc_final: 0.8711 (tp) REVERT: K 147 MET cc_start: 0.7346 (mtt) cc_final: 0.6481 (mtt) REVERT: L 42 SER cc_start: 0.8048 (m) cc_final: 0.7757 (p) REVERT: M 1 MET cc_start: 0.6494 (mtt) cc_final: 0.5516 (ppp) outliers start: 18 outliers final: 14 residues processed: 176 average time/residue: 0.2667 time to fit residues: 67.8869 Evaluate side-chains 175 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 94 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14574 Z= 0.257 Angle : 0.592 7.341 20964 Z= 0.348 Chirality : 0.036 0.152 2410 Planarity : 0.004 0.054 1663 Dihedral : 29.691 177.149 4261 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.98 % Allowed : 17.97 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % 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: 2.09 (0.28), residues: 988 helix: 2.45 (0.21), residues: 643 sheet: -0.91 (0.99), residues: 28 loop : -0.68 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 33 HIS 0.004 0.001 HIS D 82 PHE 0.011 0.001 PHE E 67 TYR 0.046 0.002 TYR D 83 ARG 0.006 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8408 (tt0) cc_final: 0.8169 (tt0) REVERT: C 64 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8249 (tm-30) REVERT: C 65 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9279 (mm) REVERT: C 95 LYS cc_start: 0.9135 (tptt) cc_final: 0.8774 (tppt) REVERT: D 63 ASN cc_start: 0.9245 (OUTLIER) cc_final: 0.8565 (m-40) REVERT: D 68 ASP cc_start: 0.8925 (t70) cc_final: 0.8661 (t0) REVERT: E 94 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8096 (mt-10) REVERT: F 22 LEU cc_start: 0.7930 (pt) cc_final: 0.7677 (tt) REVERT: G 56 GLU cc_start: 0.8582 (tt0) cc_final: 0.8284 (tt0) REVERT: G 73 ASN cc_start: 0.9117 (t0) cc_final: 0.8774 (t0) REVERT: G 89 ASN cc_start: 0.8868 (m-40) cc_final: 0.8585 (m-40) REVERT: H 37 TYR cc_start: 0.8798 (m-80) cc_final: 0.8508 (m-80) REVERT: H 76 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8220 (mm-30) REVERT: H 79 ARG cc_start: 0.8412 (ttm110) cc_final: 0.7922 (ttm110) REVERT: K 89 LEU cc_start: 0.8954 (mt) cc_final: 0.8637 (tp) REVERT: K 147 MET cc_start: 0.7372 (mtt) cc_final: 0.6510 (mtt) REVERT: L 20 MET cc_start: 0.7185 (mmt) cc_final: 0.6784 (mpp) REVERT: L 42 SER cc_start: 0.8067 (m) cc_final: 0.7774 (p) outliers start: 16 outliers final: 13 residues processed: 181 average time/residue: 0.2641 time to fit residues: 69.0780 Evaluate side-chains 178 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 111 optimal weight: 0.0970 chunk 73 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14574 Z= 0.185 Angle : 0.581 7.996 20964 Z= 0.340 Chirality : 0.035 0.164 2410 Planarity : 0.004 0.063 1663 Dihedral : 29.485 177.451 4261 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.61 % Allowed : 19.08 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % 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: 2.20 (0.28), residues: 988 helix: 2.51 (0.21), residues: 642 sheet: -0.77 (0.97), residues: 28 loop : -0.58 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 141 HIS 0.002 0.000 HIS K 75 PHE 0.010 0.001 PHE A 67 TYR 0.018 0.001 TYR D 83 ARG 0.005 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8370 (m-80) cc_final: 0.7982 (m-80) REVERT: C 56 GLU cc_start: 0.8383 (tt0) cc_final: 0.8176 (tt0) REVERT: C 64 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8268 (tm-30) REVERT: C 65 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9280 (mm) REVERT: C 68 ASN cc_start: 0.8557 (m-40) cc_final: 0.7964 (m-40) REVERT: C 95 LYS cc_start: 0.9087 (tptt) cc_final: 0.8771 (tppt) REVERT: D 68 ASP cc_start: 0.8886 (t70) cc_final: 0.8526 (t0) REVERT: E 94 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8035 (mt-10) REVERT: F 22 LEU cc_start: 0.7861 (pt) cc_final: 0.7635 (tt) REVERT: G 56 GLU cc_start: 0.8548 (tt0) cc_final: 0.8264 (tt0) REVERT: G 73 ASN cc_start: 0.9072 (t0) cc_final: 0.8720 (t0) REVERT: G 89 ASN cc_start: 0.8886 (m-40) cc_final: 0.8659 (m-40) REVERT: H 37 TYR cc_start: 0.8778 (m-80) cc_final: 0.8538 (m-80) REVERT: H 79 ARG cc_start: 0.8356 (ttm110) cc_final: 0.7843 (ttm110) REVERT: K 89 LEU cc_start: 0.8876 (mt) cc_final: 0.8589 (tp) REVERT: L 20 MET cc_start: 0.7168 (mmt) cc_final: 0.6789 (mpp) REVERT: L 42 SER cc_start: 0.8089 (m) cc_final: 0.7794 (p) outliers start: 13 outliers final: 9 residues processed: 188 average time/residue: 0.2692 time to fit residues: 72.8102 Evaluate side-chains 182 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 67 LEU 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: 5.9990 chunk 82 optimal weight: 7.9990 chunk 124 optimal weight: 50.0000 chunk 114 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 47 GLN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14574 Z= 0.291 Angle : 0.607 6.849 20964 Z= 0.355 Chirality : 0.036 0.145 2410 Planarity : 0.004 0.059 1663 Dihedral : 29.567 176.237 4259 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.61 % Allowed : 20.20 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % 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: 2.11 (0.28), residues: 988 helix: 2.43 (0.21), residues: 643 sheet: -0.75 (1.00), residues: 28 loop : -0.60 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 33 HIS 0.003 0.001 HIS M 68 PHE 0.010 0.001 PHE E 67 TYR 0.025 0.002 TYR F 88 ARG 0.010 0.000 ARG D 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8420 (tt0) cc_final: 0.8185 (tt0) REVERT: C 64 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8278 (tm-30) REVERT: C 65 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9275 (mm) REVERT: C 95 LYS cc_start: 0.9143 (tptt) cc_final: 0.8789 (tppt) REVERT: D 68 ASP cc_start: 0.8972 (t70) cc_final: 0.8693 (t0) REVERT: E 94 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8066 (mt-10) REVERT: F 22 LEU cc_start: 0.7925 (pt) cc_final: 0.7676 (tt) REVERT: G 56 GLU cc_start: 0.8573 (tt0) cc_final: 0.8284 (tt0) REVERT: G 73 ASN cc_start: 0.9108 (t0) cc_final: 0.8740 (t0) REVERT: G 89 ASN cc_start: 0.8884 (m-40) cc_final: 0.8586 (m-40) REVERT: H 37 TYR cc_start: 0.8831 (m-80) cc_final: 0.8366 (m-80) REVERT: H 79 ARG cc_start: 0.8367 (ttm110) cc_final: 0.8155 (ttm110) REVERT: K 147 MET cc_start: 0.7312 (mtt) cc_final: 0.6443 (mtt) REVERT: L 20 MET cc_start: 0.7123 (mmt) cc_final: 0.6613 (mpp) REVERT: L 42 SER cc_start: 0.8101 (m) cc_final: 0.7833 (p) outliers start: 13 outliers final: 11 residues processed: 173 average time/residue: 0.2583 time to fit residues: 65.0229 Evaluate side-chains 173 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 67 LEU 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: 6.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 0.0470 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.060851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.041255 restraints weight = 82829.414| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.39 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14574 Z= 0.184 Angle : 0.588 7.719 20964 Z= 0.343 Chirality : 0.035 0.150 2410 Planarity : 0.004 0.062 1663 Dihedral : 29.513 176.377 4259 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.49 % Allowed : 20.69 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % 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: 2.13 (0.28), residues: 988 helix: 2.45 (0.21), residues: 641 sheet: -0.78 (0.97), residues: 28 loop : -0.57 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 141 HIS 0.002 0.000 HIS D 49 PHE 0.010 0.001 PHE A 67 TYR 0.021 0.001 TYR F 88 ARG 0.012 0.000 ARG D 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2507.32 seconds wall clock time: 46 minutes 44.21 seconds (2804.21 seconds total)