Starting phenix.real_space_refine on Sat Oct 11 11:33:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7j_38100/10_2025/8x7j_38100.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7j_38100/10_2025/8x7j_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/cci-nas-00/data/ceres_data/8x7j_38100/10_2025/8x7j_38100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7j_38100/10_2025/8x7j_38100.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7j_38100/10_2025/8x7j_38100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7j_38100/10_2025/8x7j_38100.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'ARG:plan': 5, 'GLU:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} 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: {'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 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, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} 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: 3.00, per 1000 atoms: 0.22 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: 1.23 Conformation dependent library (CDL) restraints added in 449.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.15 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: 2.47 Time building geometry restraints manager: 1.65 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.330 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.160 ------------------------------------------------------------------------------- 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 14582 Z= 0.149 Angle : 0.517 5.210 20973 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG G 42 TYR 0.008 0.001 TYR F 72 PHE 0.008 0.001 PHE E 67 TRP 0.005 0.001 TRP K 93 HIS 0.002 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00312 (14574) covalent geometry : angle 0.51640 (20964) hydrogen bonds : bond 0.12179 ( 823) hydrogen bonds : angle 3.69416 ( 2018) metal coordination : bond 0.00815 ( 8) metal coordination : angle 1.56213 ( 9) *********************** 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 : 0.388 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: 0.1619 time to fit residues: 57.2305 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 : 0.386 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 D 47 GLN D 82 HIS ** D 109 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.059194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.039935 restraints weight = 83634.287| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.35 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14582 Z= 0.267 Angle : 0.619 9.590 20973 Z= 0.359 Chirality : 0.038 0.155 2410 Planarity : 0.005 0.074 1663 Dihedral : 29.899 177.993 4274 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.10 % Allowed : 11.28 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.27), residues: 988 helix: 2.54 (0.21), residues: 641 sheet: 0.23 (1.22), residues: 23 loop : -0.52 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 86 TYR 0.023 0.002 TYR D 83 PHE 0.009 0.001 PHE C 25 TRP 0.006 0.001 TRP L 61 HIS 0.004 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00592 (14574) covalent geometry : angle 0.61560 (20964) hydrogen bonds : bond 0.08545 ( 823) hydrogen bonds : angle 3.43748 ( 2018) metal coordination : bond 0.01221 ( 8) metal coordination : angle 3.09457 ( 9) *********************** 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 201 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9274 (mt) cc_final: 0.8961 (mp) REVERT: C 56 GLU cc_start: 0.8531 (tt0) cc_final: 0.8271 (tt0) REVERT: C 68 ASN cc_start: 0.8565 (m-40) cc_final: 0.8280 (m-40) REVERT: D 68 ASP cc_start: 0.9017 (t70) cc_final: 0.8702 (t0) REVERT: G 38 ASN cc_start: 0.7281 (t0) cc_final: 0.6888 (t0) REVERT: G 56 GLU cc_start: 0.8837 (tt0) cc_final: 0.8350 (tt0) REVERT: H 68 ASP cc_start: 0.9142 (t70) cc_final: 0.8823 (t0) REVERT: K 147 MET cc_start: 0.7711 (mtt) cc_final: 0.6805 (mtt) REVERT: L 42 SER cc_start: 0.8067 (m) cc_final: 0.7860 (p) outliers start: 25 outliers final: 20 residues processed: 190 average time/residue: 0.1310 time to fit residues: 35.3280 Evaluate side-chains 177 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 21 VAL 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 88 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 124 optimal weight: 40.0000 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 B 75 HIS D 109 HIS G 104 GLN K 7 ASN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.060365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.040574 restraints weight = 85024.874| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.46 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 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 = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14582 Z= 0.159 Angle : 0.568 9.989 20973 Z= 0.334 Chirality : 0.035 0.156 2410 Planarity : 0.004 0.049 1663 Dihedral : 29.747 178.548 4266 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.60 % Allowed : 12.02 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.28), residues: 988 helix: 2.66 (0.21), residues: 641 sheet: -0.41 (1.06), residues: 28 loop : -0.49 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.020 0.001 TYR D 83 PHE 0.009 0.001 PHE A 67 TRP 0.008 0.001 TRP K 93 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00346 (14574) covalent geometry : angle 0.56570 (20964) hydrogen bonds : bond 0.07906 ( 823) hydrogen bonds : angle 3.19166 ( 2018) metal coordination : bond 0.01060 ( 8) metal coordination : angle 2.58163 ( 9) *********************** 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 205 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8533 (tt0) cc_final: 0.8251 (tt0) REVERT: C 64 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8089 (tm-30) REVERT: C 68 ASN cc_start: 0.8560 (m-40) cc_final: 0.8199 (m-40) REVERT: D 68 ASP cc_start: 0.8977 (t70) cc_final: 0.8676 (t0) REVERT: E 94 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8266 (mt-10) REVERT: E 133 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7900 (mt-10) REVERT: G 38 ASN cc_start: 0.7400 (t0) cc_final: 0.6888 (t0) REVERT: G 56 GLU cc_start: 0.8827 (tt0) cc_final: 0.8329 (tt0) REVERT: H 51 ASP cc_start: 0.8394 (p0) cc_final: 0.8108 (p0) REVERT: H 68 ASP cc_start: 0.9142 (t70) cc_final: 0.8835 (t0) REVERT: K 147 MET cc_start: 0.7893 (mtt) cc_final: 0.7080 (mtt) REVERT: L 42 SER cc_start: 0.8102 (m) cc_final: 0.7900 (p) REVERT: M 1 MET cc_start: 0.7270 (ppp) cc_final: 0.6502 (mtp) outliers start: 21 outliers final: 13 residues processed: 195 average time/residue: 0.1275 time to fit residues: 35.8337 Evaluate side-chains 180 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 48 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 118 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.058541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.038654 restraints weight = 84619.083| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.39 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 14582 Z= 0.302 Angle : 0.630 8.648 20973 Z= 0.367 Chirality : 0.039 0.149 2410 Planarity : 0.004 0.048 1663 Dihedral : 29.855 177.274 4266 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.85 % Allowed : 13.26 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.27), residues: 988 helix: 2.37 (0.21), residues: 640 sheet: -0.25 (1.11), residues: 23 loop : -0.56 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.021 0.002 TYR D 83 PHE 0.011 0.001 PHE C 25 TRP 0.004 0.001 TRP K 33 HIS 0.004 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00678 (14574) covalent geometry : angle 0.62650 (20964) hydrogen bonds : bond 0.08562 ( 823) hydrogen bonds : angle 3.52256 ( 2018) metal coordination : bond 0.00829 ( 8) metal coordination : angle 3.30022 ( 9) *********************** 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 184 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8137 (mtm) cc_final: 0.7912 (mtp) REVERT: C 56 GLU cc_start: 0.8610 (tt0) cc_final: 0.8293 (tt0) REVERT: C 64 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8182 (tm-30) REVERT: D 63 ASN cc_start: 0.9291 (OUTLIER) cc_final: 0.8713 (m-40) REVERT: D 68 ASP cc_start: 0.9132 (t70) cc_final: 0.8856 (t0) REVERT: D 79 ARG cc_start: 0.8817 (ttm110) cc_final: 0.8531 (ttm-80) REVERT: F 22 LEU cc_start: 0.8048 (pt) cc_final: 0.7736 (tt) REVERT: F 63 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8509 (mt-10) REVERT: G 38 ASN cc_start: 0.7657 (t0) cc_final: 0.7373 (t0) REVERT: G 56 GLU cc_start: 0.8884 (tt0) cc_final: 0.8359 (tt0) REVERT: H 37 TYR cc_start: 0.9202 (m-80) cc_final: 0.8594 (m-80) REVERT: H 68 ASP cc_start: 0.9221 (t70) cc_final: 0.8903 (t0) REVERT: K 89 LEU cc_start: 0.9215 (mt) cc_final: 0.8975 (tp) outliers start: 23 outliers final: 18 residues processed: 177 average time/residue: 0.1252 time to fit residues: 32.0069 Evaluate side-chains 171 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 21 VAL Chi-restraints excluded: chain B residue 22 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 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 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 K residue 105 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 51 CYS 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 118 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.060158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.040240 restraints weight = 83977.426| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.45 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 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 = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14582 Z= 0.159 Angle : 0.569 8.585 20973 Z= 0.335 Chirality : 0.035 0.152 2410 Planarity : 0.004 0.053 1663 Dihedral : 29.743 178.211 4262 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.86 % Allowed : 16.36 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.28), residues: 988 helix: 2.53 (0.21), residues: 642 sheet: -0.86 (0.97), residues: 28 loop : -0.48 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.024 0.002 TYR D 83 PHE 0.011 0.001 PHE A 67 TRP 0.003 0.001 TRP K 141 HIS 0.002 0.000 HIS K 75 Details of bonding type rmsd covalent geometry : bond 0.00348 (14574) covalent geometry : angle 0.56654 (20964) hydrogen bonds : bond 0.07957 ( 823) hydrogen bonds : angle 3.19252 ( 2018) metal coordination : bond 0.00669 ( 8) metal coordination : angle 2.42782 ( 9) *********************** 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 192 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8721 (m-30) cc_final: 0.8413 (m-30) REVERT: B 63 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8414 (mt-10) REVERT: B 77 LYS cc_start: 0.9347 (mtmm) cc_final: 0.8865 (mtmm) REVERT: C 56 GLU cc_start: 0.8595 (tt0) cc_final: 0.8277 (tt0) REVERT: C 64 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8184 (tm-30) REVERT: C 68 ASN cc_start: 0.8617 (m-40) cc_final: 0.8024 (m-40) REVERT: C 91 GLU cc_start: 0.8048 (pm20) cc_final: 0.7725 (pm20) REVERT: C 92 GLU cc_start: 0.8405 (mp0) cc_final: 0.8007 (mp0) REVERT: D 63 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.8649 (m-40) REVERT: D 68 ASP cc_start: 0.9039 (t70) cc_final: 0.8751 (t0) REVERT: E 94 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8306 (mt-10) REVERT: F 22 LEU cc_start: 0.8098 (pt) cc_final: 0.7807 (tt) REVERT: F 63 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8454 (mt-10) REVERT: G 38 ASN cc_start: 0.7452 (t0) cc_final: 0.7222 (t0) REVERT: G 56 GLU cc_start: 0.8889 (tt0) cc_final: 0.8360 (tt0) REVERT: G 89 ASN cc_start: 0.9014 (m-40) cc_final: 0.8704 (m-40) REVERT: H 37 TYR cc_start: 0.9160 (m-80) cc_final: 0.8739 (m-80) REVERT: H 68 ASP cc_start: 0.9154 (t70) cc_final: 0.8870 (t0) REVERT: H 93 GLU cc_start: 0.8910 (mp0) cc_final: 0.8515 (mp0) REVERT: K 89 LEU cc_start: 0.9202 (mt) cc_final: 0.8977 (tp) REVERT: L 20 MET cc_start: 0.7569 (mmt) cc_final: 0.7214 (mpp) REVERT: M 1 MET cc_start: 0.6487 (mtp) cc_final: 0.5322 (ppp) outliers start: 15 outliers final: 11 residues processed: 186 average time/residue: 0.1185 time to fit residues: 32.4839 Evaluate side-chains 177 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN 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 105 SER Chi-restraints excluded: chain K residue 120 VAL 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 107 optimal weight: 40.0000 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** G 104 GLN ** 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 = 0.3666 r_free = 0.3666 target = 0.060218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.040358 restraints weight = 83806.576| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.41 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14582 Z= 0.161 Angle : 0.564 7.928 20973 Z= 0.333 Chirality : 0.035 0.142 2410 Planarity : 0.004 0.056 1663 Dihedral : 29.606 177.915 4261 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.86 % Allowed : 16.48 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.27), residues: 988 helix: 2.50 (0.21), residues: 642 sheet: -0.69 (0.99), residues: 28 loop : -0.46 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.034 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 TRP 0.004 0.001 TRP K 141 HIS 0.002 0.000 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00354 (14574) covalent geometry : angle 0.56197 (20964) hydrogen bonds : bond 0.07832 ( 823) hydrogen bonds : angle 3.17098 ( 2018) metal coordination : bond 0.00524 ( 8) metal coordination : angle 2.20679 ( 9) *********************** 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 190 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8459 (mt-10) REVERT: B 77 LYS cc_start: 0.9323 (mtmm) cc_final: 0.8876 (mtmm) REVERT: C 56 GLU cc_start: 0.8556 (tt0) cc_final: 0.8274 (tt0) REVERT: C 64 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8229 (tm-30) REVERT: D 68 ASP cc_start: 0.9040 (t70) cc_final: 0.8749 (t0) REVERT: E 94 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8277 (mt-10) REVERT: F 22 LEU cc_start: 0.8164 (pt) cc_final: 0.7896 (tt) REVERT: F 63 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8402 (mt-10) REVERT: G 38 ASN cc_start: 0.7401 (t0) cc_final: 0.7186 (t0) REVERT: G 56 GLU cc_start: 0.8863 (tt0) cc_final: 0.8340 (tt0) REVERT: G 89 ASN cc_start: 0.9021 (m-40) cc_final: 0.8697 (m-40) REVERT: H 37 TYR cc_start: 0.9155 (m-80) cc_final: 0.8741 (m-80) REVERT: H 68 ASP cc_start: 0.9140 (t70) cc_final: 0.8852 (t0) REVERT: H 79 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7903 (mtm-85) REVERT: K 89 LEU cc_start: 0.9136 (mt) cc_final: 0.8916 (tp) REVERT: M 1 MET cc_start: 0.6462 (mtp) cc_final: 0.5166 (ppp) outliers start: 15 outliers final: 12 residues processed: 184 average time/residue: 0.1176 time to fit residues: 31.9613 Evaluate side-chains 176 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 E residue 105 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 104 GLN 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 41 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** G 104 GLN ** 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 = 0.3646 r_free = 0.3646 target = 0.059303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.039314 restraints weight = 85448.039| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.42 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14582 Z= 0.226 Angle : 0.590 7.466 20973 Z= 0.346 Chirality : 0.036 0.180 2410 Planarity : 0.004 0.055 1663 Dihedral : 29.666 176.952 4259 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.86 % Allowed : 17.97 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.28), residues: 988 helix: 2.44 (0.21), residues: 643 sheet: -0.79 (1.01), residues: 28 loop : -0.59 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 88 TYR 0.026 0.002 TYR D 83 PHE 0.010 0.001 PHE E 67 TRP 0.004 0.001 TRP K 33 HIS 0.003 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00504 (14574) covalent geometry : angle 0.58767 (20964) hydrogen bonds : bond 0.07864 ( 823) hydrogen bonds : angle 3.29574 ( 2018) metal coordination : bond 0.00562 ( 8) metal coordination : angle 2.76636 ( 9) *********************** 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 184 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.7969 (mtm) cc_final: 0.7736 (mtt) REVERT: C 56 GLU cc_start: 0.8592 (tt0) cc_final: 0.8293 (tt0) REVERT: C 64 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8182 (tm-30) REVERT: D 63 ASN cc_start: 0.9304 (OUTLIER) cc_final: 0.8648 (m-40) REVERT: D 68 ASP cc_start: 0.9131 (t70) cc_final: 0.8852 (t0) REVERT: E 94 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8308 (mt-10) REVERT: F 22 LEU cc_start: 0.8178 (pt) cc_final: 0.7907 (tt) REVERT: F 63 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8419 (mt-10) REVERT: G 56 GLU cc_start: 0.8868 (tt0) cc_final: 0.8294 (tt0) REVERT: G 89 ASN cc_start: 0.9021 (m-40) cc_final: 0.8712 (m-40) REVERT: H 37 TYR cc_start: 0.9195 (m-80) cc_final: 0.8751 (m-80) REVERT: H 68 ASP cc_start: 0.9147 (t70) cc_final: 0.8870 (t0) REVERT: H 93 GLU cc_start: 0.8850 (mp0) cc_final: 0.8606 (mp0) REVERT: K 89 LEU cc_start: 0.9195 (mt) cc_final: 0.8973 (tp) REVERT: L 20 MET cc_start: 0.7385 (mmt) cc_final: 0.7019 (mpp) REVERT: M 1 MET cc_start: 0.6535 (mtp) cc_final: 0.5141 (ppp) outliers start: 15 outliers final: 13 residues processed: 179 average time/residue: 0.1224 time to fit residues: 32.0221 Evaluate side-chains 175 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 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 66 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 105 SER 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 45 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- 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** G 38 ASN G 104 GLN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.060324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.040538 restraints weight = 83632.345| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.38 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 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 = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14582 Z= 0.152 Angle : 0.567 7.314 20973 Z= 0.334 Chirality : 0.034 0.173 2410 Planarity : 0.004 0.058 1663 Dihedral : 29.585 177.415 4259 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.11 % Allowed : 17.60 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.28), residues: 988 helix: 2.47 (0.21), residues: 643 sheet: -0.67 (1.00), residues: 28 loop : -0.60 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.025 0.001 TYR D 83 PHE 0.011 0.001 PHE A 67 TRP 0.005 0.001 TRP K 141 HIS 0.001 0.000 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00330 (14574) covalent geometry : angle 0.56516 (20964) hydrogen bonds : bond 0.07861 ( 823) hydrogen bonds : angle 3.12087 ( 2018) metal coordination : bond 0.00453 ( 8) metal coordination : angle 2.10429 ( 9) *********************** 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 189 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8538 (tt0) cc_final: 0.8265 (tt0) REVERT: C 64 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8178 (tm-30) REVERT: C 95 LYS cc_start: 0.9102 (tptt) cc_final: 0.8727 (tppt) REVERT: D 63 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8515 (m-40) REVERT: D 68 ASP cc_start: 0.9074 (t70) cc_final: 0.8696 (t0) REVERT: E 94 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8287 (mt-10) REVERT: F 22 LEU cc_start: 0.8160 (pt) cc_final: 0.7889 (tt) REVERT: F 63 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8348 (mt-10) REVERT: G 56 GLU cc_start: 0.8857 (tt0) cc_final: 0.8341 (tt0) REVERT: G 89 ASN cc_start: 0.9029 (m-40) cc_final: 0.8682 (m-40) REVERT: H 37 TYR cc_start: 0.9174 (m-80) cc_final: 0.8721 (m-80) REVERT: H 68 ASP cc_start: 0.9128 (t70) cc_final: 0.8879 (t0) REVERT: H 76 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8202 (mm-30) REVERT: H 93 GLU cc_start: 0.8807 (mp0) cc_final: 0.8557 (mp0) REVERT: K 89 LEU cc_start: 0.9119 (mt) cc_final: 0.8885 (tp) REVERT: L 20 MET cc_start: 0.7298 (mmt) cc_final: 0.6918 (mpp) REVERT: M 1 MET cc_start: 0.6355 (mtp) cc_final: 0.5161 (ppp) outliers start: 17 outliers final: 13 residues processed: 182 average time/residue: 0.1194 time to fit residues: 32.1067 Evaluate side-chains 183 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 105 SER 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 26 optimal weight: 3.9990 chunk 118 optimal weight: 30.0000 chunk 20 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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** G 38 ASN ** 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 = 0.3657 r_free = 0.3657 target = 0.059730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.039838 restraints weight = 84739.373| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.41 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14582 Z= 0.197 Angle : 0.587 7.674 20973 Z= 0.343 Chirality : 0.035 0.167 2410 Planarity : 0.004 0.057 1663 Dihedral : 29.578 177.062 4259 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.11 % Allowed : 18.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.28), residues: 988 helix: 2.44 (0.21), residues: 643 sheet: -0.72 (1.00), residues: 28 loop : -0.64 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.028 0.002 TYR D 83 PHE 0.010 0.001 PHE E 67 TRP 0.004 0.001 TRP K 141 HIS 0.002 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00439 (14574) covalent geometry : angle 0.58550 (20964) hydrogen bonds : bond 0.07794 ( 823) hydrogen bonds : angle 3.20981 ( 2018) metal coordination : bond 0.00501 ( 8) metal coordination : angle 2.40801 ( 9) *********************** 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 188 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8544 (tt0) cc_final: 0.8277 (tt0) REVERT: C 64 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8217 (tm-30) REVERT: C 95 LYS cc_start: 0.9143 (tptt) cc_final: 0.8767 (tppt) REVERT: D 63 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.8569 (m-40) REVERT: D 68 ASP cc_start: 0.9111 (t70) cc_final: 0.8746 (t0) REVERT: E 94 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8307 (mt-10) REVERT: F 22 LEU cc_start: 0.8181 (pt) cc_final: 0.7915 (tt) REVERT: F 63 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8355 (mt-10) REVERT: G 56 GLU cc_start: 0.8839 (tt0) cc_final: 0.8286 (tt0) REVERT: G 73 ASN cc_start: 0.9296 (t0) cc_final: 0.8890 (t0) REVERT: G 89 ASN cc_start: 0.9051 (m-40) cc_final: 0.8733 (m-40) REVERT: H 37 TYR cc_start: 0.9159 (m-80) cc_final: 0.8704 (m-80) REVERT: H 68 ASP cc_start: 0.9134 (t70) cc_final: 0.8894 (t0) REVERT: H 93 GLU cc_start: 0.8823 (mp0) cc_final: 0.8569 (mp0) REVERT: K 89 LEU cc_start: 0.9151 (mt) cc_final: 0.8902 (tp) REVERT: L 20 MET cc_start: 0.7272 (mmt) cc_final: 0.6929 (mpp) REVERT: M 1 MET cc_start: 0.6454 (mtp) cc_final: 0.5216 (ppp) outliers start: 17 outliers final: 15 residues processed: 179 average time/residue: 0.1214 time to fit residues: 32.0468 Evaluate side-chains 186 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 D residue 63 ASN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 38 ASN 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 105 SER 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 12 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 103 optimal weight: 0.0030 chunk 68 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 0.0670 chunk 47 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 overall best weight: 0.3406 ------------------------------------------------------------------------------- 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** G 38 ASN ** 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 = 0.3689 r_free = 0.3689 target = 0.061190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.041444 restraints weight = 83449.261| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.43 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14582 Z= 0.144 Angle : 0.585 8.686 20973 Z= 0.340 Chirality : 0.035 0.162 2410 Planarity : 0.004 0.058 1663 Dihedral : 29.440 177.295 4259 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.49 % Allowed : 19.58 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.28), residues: 988 helix: 2.44 (0.21), residues: 642 sheet: -0.46 (1.00), residues: 28 loop : -0.56 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.038 0.002 TYR G 39 PHE 0.010 0.001 PHE A 67 TRP 0.007 0.001 TRP K 141 HIS 0.002 0.000 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00309 (14574) covalent geometry : angle 0.58375 (20964) hydrogen bonds : bond 0.08310 ( 823) hydrogen bonds : angle 3.00847 ( 2018) metal coordination : bond 0.00370 ( 8) metal coordination : angle 1.60633 ( 9) ********************** 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 196 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6435 (m-80) cc_final: 0.5938 (m-80) REVERT: B 63 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7907 (mt-10) REVERT: C 56 GLU cc_start: 0.8544 (tt0) cc_final: 0.8270 (tt0) REVERT: C 64 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8203 (tm-30) REVERT: C 68 ASN cc_start: 0.8548 (m-40) cc_final: 0.7911 (m-40) REVERT: C 95 LYS cc_start: 0.9159 (tptt) cc_final: 0.8824 (tppt) REVERT: D 35 GLU cc_start: 0.8026 (pp20) cc_final: 0.7821 (pp20) REVERT: D 68 ASP cc_start: 0.9082 (t70) cc_final: 0.8711 (t0) REVERT: E 94 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8338 (mt-10) REVERT: F 22 LEU cc_start: 0.8148 (pt) cc_final: 0.7897 (tt) REVERT: F 63 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8311 (mt-10) REVERT: G 56 GLU cc_start: 0.8867 (tt0) cc_final: 0.8340 (tt0) REVERT: G 89 ASN cc_start: 0.9067 (m-40) cc_final: 0.8758 (m-40) REVERT: H 37 TYR cc_start: 0.9178 (m-80) cc_final: 0.8751 (m-80) REVERT: H 68 ASP cc_start: 0.9134 (t70) cc_final: 0.8874 (t0) REVERT: H 93 GLU cc_start: 0.8808 (mp0) cc_final: 0.8548 (mp0) REVERT: K 89 LEU cc_start: 0.9139 (mt) cc_final: 0.8865 (tp) REVERT: L 20 MET cc_start: 0.7344 (mmt) cc_final: 0.7042 (mpp) REVERT: M 1 MET cc_start: 0.6469 (mtp) cc_final: 0.5490 (ppp) outliers start: 12 outliers final: 9 residues processed: 190 average time/residue: 0.1191 time to fit residues: 33.0062 Evaluate side-chains 178 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 96 THR Chi-restraints excluded: chain F residue 21 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 35 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 63 ASN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.059726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.039780 restraints weight = 85391.712| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.39 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14582 Z= 0.219 Angle : 0.599 7.446 20973 Z= 0.349 Chirality : 0.036 0.149 2410 Planarity : 0.004 0.057 1663 Dihedral : 29.533 176.168 4255 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.49 % Allowed : 19.58 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.28), residues: 988 helix: 2.43 (0.21), residues: 644 sheet: -0.61 (1.01), residues: 28 loop : -0.58 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.085 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.004 0.001 TRP K 33 HIS 0.002 0.001 HIS M 68 Details of bonding type rmsd covalent geometry : bond 0.00489 (14574) covalent geometry : angle 0.59736 (20964) hydrogen bonds : bond 0.07873 ( 823) hydrogen bonds : angle 3.23775 ( 2018) metal coordination : bond 0.00500 ( 8) metal coordination : angle 2.40947 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2983.44 seconds wall clock time: 51 minutes 57.88 seconds (3117.88 seconds total)