Starting phenix.real_space_refine on Sun Jan 19 21:12:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7j_38100/01_2025/8x7j_38100.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7j_38100/01_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_38100/01_2025/8x7j_38100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7j_38100/01_2025/8x7j_38100.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7j_38100/01_2025/8x7j_38100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7j_38100/01_2025/8x7j_38100.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1025 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 288 5.49 5 S 25 5.16 5 C 7736 2.51 5 N 2547 2.21 5 O 3141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13739 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 642 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2967 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2937 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "K" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1031 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 126} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "L" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 405 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 399 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 56} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13064 SG CYS L 31 59.328 67.509 25.982 1.00218.04 S ATOM 13203 SG CYS L 51 60.840 71.001 26.041 1.00210.14 S ATOM 13227 SG CYS L 54 57.120 70.534 25.078 1.00213.50 S ATOM 12959 SG CYS L 16 71.165 67.606 21.224 1.00283.03 S ATOM 12977 SG CYS L 19 74.736 68.117 20.046 1.00282.47 S ATOM 13100 SG CYS L 36 74.096 65.680 22.767 1.00253.66 S ATOM 13118 SG CYS L 39 73.702 69.387 23.482 1.00248.31 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 75 " occ=0.45 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.45 Time building chain proxies: 7.40, per 1000 atoms: 0.54 Number of scatterers: 13739 At special positions: 0 Unit cell: (118.14, 125.658, 112.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 25 16.00 P 288 15.00 O 3141 8.00 N 2547 7.00 C 7736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 33 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 54 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 16 " Number of angles added : 9 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1918 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 13 sheets defined 63.1% alpha, 4.4% beta 143 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 6.65 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.515A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.870A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.472A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.310A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.522A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 29 removed outlier: 4.026A pdb=" N ASN F 25 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.886A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.730A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.526A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 3 through 16 Processing helix chain 'K' and resid 86 through 91 Processing helix chain 'K' and resid 98 through 112 Processing helix chain 'K' and resid 120 through 130 Processing helix chain 'K' and resid 130 through 145 Processing helix chain 'L' and resid 36 through 44 Processing helix chain 'L' and resid 58 through 67 removed outlier: 3.859A pdb=" N ARG L 67 " --> pdb=" O ARG L 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.965A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.940A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.911A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.307A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 32 through 38 Processing sheet with id=AB3, first strand: chain 'L' and resid 27 through 28 Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 6 removed outlier: 5.969A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 478 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 3.85 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.410 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14574 Z= 0.174 Angle : 0.516 5.210 20964 Z= 0.317 Chirality : 0.033 0.131 2410 Planarity : 0.003 0.034 1663 Dihedral : 25.848 178.758 6090 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.73 % Allowed : 4.46 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.28), residues: 988 helix: 2.81 (0.21), residues: 636 sheet: -0.95 (0.96), residues: 28 loop : -0.35 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 93 HIS 0.002 0.001 HIS M 68 PHE 0.008 0.001 PHE E 67 TYR 0.008 0.001 TYR F 72 ARG 0.002 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 253 time to evaluate : 1.203 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: 0.3652 time to fit residues: 129.9884 Evaluate side-chains 187 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 56 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 63 optimal weight: 0.0030 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 64 ASN B 75 HIS D 47 GLN D 109 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.061532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.042111 restraints weight = 82357.593| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.42 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 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 = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14574 Z= 0.178 Angle : 0.565 9.156 20964 Z= 0.331 Chirality : 0.035 0.148 2410 Planarity : 0.004 0.034 1663 Dihedral : 29.675 178.942 4274 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.23 % Allowed : 11.77 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.27), residues: 988 helix: 2.70 (0.21), residues: 642 sheet: -0.42 (1.05), residues: 28 loop : -0.45 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 141 HIS 0.002 0.001 HIS D 109 PHE 0.008 0.001 PHE A 67 TYR 0.028 0.002 TYR D 83 ARG 0.008 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8712 (mt0) cc_final: 0.8508 (mt0) REVERT: B 49 LEU cc_start: 0.9272 (mt) cc_final: 0.8902 (mp) REVERT: B 88 TYR cc_start: 0.8965 (m-10) cc_final: 0.8348 (m-10) REVERT: C 56 GLU cc_start: 0.8531 (tt0) cc_final: 0.8239 (tt0) REVERT: C 68 ASN cc_start: 0.8652 (m-40) cc_final: 0.8346 (m-40) REVERT: D 51 ASP cc_start: 0.8344 (p0) cc_final: 0.8130 (p0) REVERT: D 67 ASN cc_start: 0.9127 (m-40) cc_final: 0.8857 (m-40) REVERT: D 68 ASP cc_start: 0.8885 (t70) cc_final: 0.8576 (t0) REVERT: D 93 GLU cc_start: 0.8683 (mp0) cc_final: 0.8385 (mp0) REVERT: E 94 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8250 (mt-10) REVERT: G 38 ASN cc_start: 0.7105 (t0) cc_final: 0.6677 (t0) REVERT: G 56 GLU cc_start: 0.8848 (tt0) cc_final: 0.8371 (tt0) REVERT: G 87 ILE cc_start: 0.9504 (mt) cc_final: 0.9287 (mp) REVERT: H 68 ASP cc_start: 0.9121 (t70) cc_final: 0.8791 (t0) REVERT: H 79 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7835 (mtm-85) REVERT: H 113 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8734 (mt-10) REVERT: K 147 MET cc_start: 0.7920 (mtt) cc_final: 0.7094 (mtt) REVERT: L 42 SER cc_start: 0.8164 (m) cc_final: 0.7923 (p) REVERT: M 1 MET cc_start: 0.7685 (ptt) cc_final: 0.6715 (ppp) outliers start: 18 outliers final: 13 residues processed: 205 average time/residue: 0.2792 time to fit residues: 81.1521 Evaluate side-chains 186 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 3 optimal weight: 2.9990 chunk 102 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 64 ASN D 82 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.059361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.039586 restraints weight = 85419.818| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.43 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 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 = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14574 Z= 0.315 Angle : 0.596 9.307 20964 Z= 0.349 Chirality : 0.037 0.157 2410 Planarity : 0.004 0.048 1663 Dihedral : 29.739 177.539 4262 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.60 % Allowed : 12.39 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.28), residues: 988 helix: 2.62 (0.21), residues: 643 sheet: 0.28 (1.18), residues: 23 loop : -0.43 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 93 HIS 0.004 0.001 HIS M 68 PHE 0.010 0.001 PHE C 25 TYR 0.028 0.002 TYR D 83 ARG 0.004 0.001 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8262 (tp30) cc_final: 0.8048 (tm-30) REVERT: C 56 GLU cc_start: 0.8601 (tt0) cc_final: 0.8303 (tt0) REVERT: C 64 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8053 (tm-30) REVERT: C 65 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9231 (mm) REVERT: C 68 ASN cc_start: 0.8559 (m-40) cc_final: 0.8149 (m-40) REVERT: D 68 ASP cc_start: 0.9046 (t70) cc_final: 0.8753 (t0) REVERT: D 93 GLU cc_start: 0.8796 (mp0) cc_final: 0.8469 (mp0) REVERT: E 94 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8188 (mt-10) REVERT: F 22 LEU cc_start: 0.8083 (pt) cc_final: 0.7802 (tt) REVERT: G 38 ASN cc_start: 0.7459 (t0) cc_final: 0.7065 (t0) REVERT: G 56 GLU cc_start: 0.8832 (tt0) cc_final: 0.8315 (tt0) REVERT: G 92 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8670 (mt-10) REVERT: H 68 ASP cc_start: 0.9162 (t70) cc_final: 0.8837 (t0) REVERT: K 147 MET cc_start: 0.7769 (mtt) cc_final: 0.6889 (mtt) REVERT: L 42 SER cc_start: 0.7888 (m) cc_final: 0.7687 (p) REVERT: M 1 MET cc_start: 0.7867 (ptt) cc_final: 0.6822 (mtp) outliers start: 21 outliers final: 16 residues processed: 184 average time/residue: 0.2612 time to fit residues: 69.3272 Evaluate side-chains 175 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain 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 115 optimal weight: 10.0000 chunk 106 optimal weight: 30.0000 chunk 57 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS ** 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 = 0.3659 r_free = 0.3659 target = 0.059689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.039912 restraints weight = 83603.196| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.40 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 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 = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14574 Z= 0.258 Angle : 0.576 9.048 20964 Z= 0.340 Chirality : 0.036 0.157 2410 Planarity : 0.004 0.054 1663 Dihedral : 29.727 178.098 4262 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.97 % Allowed : 13.51 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.27), residues: 988 helix: 2.55 (0.21), residues: 643 sheet: -0.61 (1.02), residues: 28 loop : -0.44 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 33 HIS 0.003 0.001 HIS M 68 PHE 0.010 0.001 PHE E 67 TYR 0.018 0.001 TYR D 83 ARG 0.005 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8347 (tp30) cc_final: 0.8084 (tm-30) REVERT: C 56 GLU cc_start: 0.8604 (tt0) cc_final: 0.8290 (tt0) REVERT: C 64 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8072 (tm-30) REVERT: C 65 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9263 (mm) REVERT: C 68 ASN cc_start: 0.8586 (m-40) cc_final: 0.8082 (m-40) REVERT: D 63 ASN cc_start: 0.9312 (OUTLIER) cc_final: 0.8728 (m-40) REVERT: D 68 ASP cc_start: 0.9035 (t70) cc_final: 0.8740 (t0) REVERT: D 93 GLU cc_start: 0.8819 (mp0) cc_final: 0.8427 (mp0) REVERT: E 94 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8164 (mt-10) REVERT: F 22 LEU cc_start: 0.8170 (pt) cc_final: 0.7894 (tt) REVERT: G 38 ASN cc_start: 0.7576 (t0) cc_final: 0.7261 (t0) REVERT: G 56 GLU cc_start: 0.8883 (tt0) cc_final: 0.8371 (tt0) REVERT: G 92 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8555 (mt-10) REVERT: H 37 TYR cc_start: 0.9054 (m-80) cc_final: 0.8622 (m-80) REVERT: H 68 ASP cc_start: 0.9166 (t70) cc_final: 0.8856 (t0) REVERT: H 79 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.7989 (mtm-85) REVERT: H 93 GLU cc_start: 0.8976 (mp0) cc_final: 0.8716 (mp0) REVERT: K 147 MET cc_start: 0.7669 (mtt) cc_final: 0.6855 (mtt) REVERT: L 42 SER cc_start: 0.7907 (m) cc_final: 0.7699 (p) outliers start: 24 outliers final: 14 residues processed: 185 average time/residue: 0.2760 time to fit residues: 73.3233 Evaluate side-chains 175 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 33 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 116 optimal weight: 30.0000 chunk 89 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.0570 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 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 = 0.3664 r_free = 0.3664 target = 0.060021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.040188 restraints weight = 84383.972| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.38 r_work (final): 0.2946 ------------------------------------------------------------------------------- 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 = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14574 Z= 0.220 Angle : 0.562 8.355 20964 Z= 0.332 Chirality : 0.035 0.150 2410 Planarity : 0.003 0.051 1663 Dihedral : 29.653 178.110 4261 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.11 % Allowed : 14.87 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.28), residues: 988 helix: 2.56 (0.21), residues: 643 sheet: -0.67 (1.01), residues: 28 loop : -0.45 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 141 HIS 0.002 0.000 HIS M 68 PHE 0.010 0.001 PHE E 67 TYR 0.014 0.001 TYR D 83 ARG 0.013 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8560 (tt0) cc_final: 0.8281 (tt0) REVERT: C 64 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8061 (tm-30) REVERT: C 65 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9248 (mm) REVERT: C 68 ASN cc_start: 0.8563 (m-40) cc_final: 0.7900 (m-40) REVERT: D 68 ASP cc_start: 0.9023 (t70) cc_final: 0.8728 (t0) REVERT: D 76 GLU cc_start: 0.9099 (tp30) cc_final: 0.8856 (tp30) REVERT: D 79 ARG cc_start: 0.8827 (ttm-80) cc_final: 0.8481 (ttm110) REVERT: E 94 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8215 (mt-10) REVERT: F 22 LEU cc_start: 0.8189 (pt) cc_final: 0.7936 (tt) REVERT: G 38 ASN cc_start: 0.7631 (t0) cc_final: 0.7321 (t0) REVERT: G 56 GLU cc_start: 0.8859 (tt0) cc_final: 0.8348 (tt0) REVERT: G 92 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8501 (mt-10) REVERT: H 37 TYR cc_start: 0.9084 (m-80) cc_final: 0.8737 (m-80) REVERT: H 68 ASP cc_start: 0.9147 (t70) cc_final: 0.8864 (t0) REVERT: H 76 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8463 (mm-30) REVERT: H 79 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.7934 (mtm-85) REVERT: K 147 MET cc_start: 0.7628 (mtt) cc_final: 0.6819 (mtt) REVERT: L 42 SER cc_start: 0.7918 (m) cc_final: 0.7710 (p) outliers start: 17 outliers final: 14 residues processed: 183 average time/residue: 0.2501 time to fit residues: 66.6232 Evaluate side-chains 180 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 95 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** ** 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 = 0.3634 r_free = 0.3634 target = 0.058755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.038752 restraints weight = 85532.076| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.41 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 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 = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 14574 Z= 0.360 Angle : 0.617 7.669 20964 Z= 0.362 Chirality : 0.038 0.155 2410 Planarity : 0.004 0.041 1663 Dihedral : 29.782 176.917 4261 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.60 % Allowed : 15.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.27), residues: 988 helix: 2.35 (0.21), residues: 643 sheet: -0.22 (1.14), residues: 23 loop : -0.54 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 93 HIS 0.004 0.001 HIS M 68 PHE 0.011 0.001 PHE F 61 TYR 0.016 0.001 TYR F 88 ARG 0.004 0.001 ARG L 55 *********************** 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 183 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8635 (tt0) cc_final: 0.8330 (tt0) REVERT: C 64 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8169 (tm-30) REVERT: C 65 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9247 (mm) REVERT: D 63 ASN cc_start: 0.9353 (OUTLIER) cc_final: 0.8787 (m-40) REVERT: D 68 ASP cc_start: 0.9105 (t70) cc_final: 0.8823 (t0) REVERT: F 22 LEU cc_start: 0.8181 (pt) cc_final: 0.7917 (tt) REVERT: G 38 ASN cc_start: 0.7600 (t0) cc_final: 0.7318 (t0) REVERT: G 56 GLU cc_start: 0.8880 (tt0) cc_final: 0.8359 (tt0) REVERT: G 92 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8510 (mt-10) REVERT: H 37 TYR cc_start: 0.9137 (m-80) cc_final: 0.8771 (m-80) REVERT: H 68 ASP cc_start: 0.9229 (t70) cc_final: 0.8932 (t0) REVERT: H 79 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.7904 (mtm-85) REVERT: H 93 GLU cc_start: 0.8980 (mp0) cc_final: 0.8632 (mp0) REVERT: L 42 SER cc_start: 0.7975 (m) cc_final: 0.7773 (p) REVERT: M 1 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.4456 (pmm) outliers start: 21 outliers final: 16 residues processed: 176 average time/residue: 0.2632 time to fit residues: 67.3416 Evaluate side-chains 176 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 1 MET 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 40 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.059724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.039769 restraints weight = 84374.397| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.38 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 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 = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14574 Z= 0.236 Angle : 0.581 7.792 20964 Z= 0.342 Chirality : 0.035 0.150 2410 Planarity : 0.004 0.047 1663 Dihedral : 29.706 177.677 4261 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.11 % Allowed : 17.47 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.28), residues: 988 helix: 2.46 (0.21), residues: 643 sheet: -0.88 (1.00), residues: 28 loop : -0.54 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 33 HIS 0.002 0.001 HIS M 68 PHE 0.011 0.001 PHE E 67 TYR 0.044 0.001 TYR D 83 ARG 0.003 0.000 ARG L 55 *********************** 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 187 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8789 (m-30) cc_final: 0.8346 (m-30) REVERT: C 56 GLU cc_start: 0.8573 (tt0) cc_final: 0.8287 (tt0) REVERT: C 64 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8099 (tm-30) REVERT: C 65 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9170 (mm) REVERT: C 95 LYS cc_start: 0.9171 (tptt) cc_final: 0.8800 (tppt) REVERT: D 35 GLU cc_start: 0.8243 (pp20) cc_final: 0.8010 (pp20) REVERT: D 63 ASN cc_start: 0.9301 (OUTLIER) cc_final: 0.8680 (m-40) REVERT: D 68 ASP cc_start: 0.9050 (t70) cc_final: 0.8766 (t0) REVERT: E 94 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8142 (mt-10) REVERT: F 22 LEU cc_start: 0.8185 (pt) cc_final: 0.7908 (tt) REVERT: G 38 ASN cc_start: 0.7685 (t0) cc_final: 0.7458 (t0) REVERT: G 56 GLU cc_start: 0.8872 (tt0) cc_final: 0.8301 (tt0) REVERT: G 92 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8479 (mt-10) REVERT: H 37 TYR cc_start: 0.9140 (m-80) cc_final: 0.8765 (m-80) REVERT: H 68 ASP cc_start: 0.9139 (t70) cc_final: 0.8862 (t0) REVERT: H 76 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8411 (mm-30) REVERT: H 79 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.7791 (mtm-85) REVERT: H 93 GLU cc_start: 0.9000 (mp0) cc_final: 0.8647 (mp0) REVERT: L 20 MET cc_start: 0.7333 (mmt) cc_final: 0.6947 (mpp) REVERT: L 42 SER cc_start: 0.7994 (m) cc_final: 0.7793 (p) REVERT: M 1 MET cc_start: 0.6258 (ptm) cc_final: 0.4603 (pmm) outliers start: 17 outliers final: 13 residues processed: 180 average time/residue: 0.2886 time to fit residues: 74.9000 Evaluate side-chains 179 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 C residue 65 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 51 CYS 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 77 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.060007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.040115 restraints weight = 83830.341| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.39 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 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 = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14574 Z= 0.214 Angle : 0.579 7.671 20964 Z= 0.340 Chirality : 0.035 0.198 2410 Planarity : 0.003 0.046 1663 Dihedral : 29.620 177.250 4261 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.11 % Allowed : 18.22 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.28), residues: 988 helix: 2.47 (0.21), residues: 643 sheet: -0.79 (0.99), residues: 28 loop : -0.50 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 141 HIS 0.002 0.001 HIS D 82 PHE 0.010 0.001 PHE E 67 TYR 0.044 0.001 TYR D 83 ARG 0.007 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8563 (tt0) cc_final: 0.8277 (tt0) REVERT: C 64 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 65 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9196 (mm) REVERT: C 95 LYS cc_start: 0.9184 (tptt) cc_final: 0.8824 (tppt) REVERT: D 63 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8573 (m-40) REVERT: D 68 ASP cc_start: 0.9046 (t70) cc_final: 0.8763 (t0) REVERT: E 94 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8138 (mt-10) REVERT: F 22 LEU cc_start: 0.8189 (pt) cc_final: 0.7933 (tt) REVERT: G 56 GLU cc_start: 0.8858 (tt0) cc_final: 0.8291 (tt0) REVERT: G 89 ASN cc_start: 0.8994 (m-40) cc_final: 0.8705 (m-40) REVERT: G 92 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8479 (mt-10) REVERT: H 37 TYR cc_start: 0.9134 (m-80) cc_final: 0.8723 (m-80) REVERT: H 68 ASP cc_start: 0.9140 (t70) cc_final: 0.8889 (t0) REVERT: H 76 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8438 (mm-30) REVERT: H 79 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.7796 (mtm-85) REVERT: H 93 GLU cc_start: 0.9006 (mp0) cc_final: 0.8658 (mp0) REVERT: L 20 MET cc_start: 0.7297 (mmt) cc_final: 0.6920 (mpp) REVERT: L 42 SER cc_start: 0.8006 (m) cc_final: 0.7800 (p) REVERT: M 1 MET cc_start: 0.6298 (ptm) cc_final: 0.4499 (pmm) outliers start: 17 outliers final: 12 residues processed: 182 average time/residue: 0.2568 time to fit residues: 68.5135 Evaluate side-chains 179 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 25 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.0060 chunk 56 optimal weight: 0.9980 chunk 109 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.060938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.041172 restraints weight = 83090.546| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.40 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 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 = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14574 Z= 0.184 Angle : 0.578 8.020 20964 Z= 0.340 Chirality : 0.034 0.173 2410 Planarity : 0.003 0.047 1663 Dihedral : 29.458 177.521 4261 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.73 % Allowed : 19.70 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.28), residues: 988 helix: 2.45 (0.21), residues: 642 sheet: -0.71 (0.98), residues: 28 loop : -0.47 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 141 HIS 0.002 0.000 HIS K 75 PHE 0.010 0.001 PHE A 67 TYR 0.021 0.001 TYR D 83 ARG 0.009 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 1.114 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: A 41 TYR cc_start: 0.6426 (m-80) cc_final: 0.5941 (m-80) REVERT: B 63 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8459 (mt-10) REVERT: C 56 GLU cc_start: 0.8549 (tt0) cc_final: 0.8283 (tt0) REVERT: C 64 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8121 (tm-30) REVERT: C 65 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9201 (mm) REVERT: C 68 ASN cc_start: 0.8547 (m-40) cc_final: 0.7899 (m-40) REVERT: C 95 LYS cc_start: 0.9153 (tptt) cc_final: 0.8814 (tppt) REVERT: D 63 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8258 (m-40) REVERT: D 67 ASN cc_start: 0.9156 (m-40) cc_final: 0.8758 (m110) REVERT: D 68 ASP cc_start: 0.9027 (t70) cc_final: 0.8649 (t0) REVERT: E 94 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8124 (mt-10) REVERT: F 22 LEU cc_start: 0.8171 (pt) cc_final: 0.7919 (tt) REVERT: G 56 GLU cc_start: 0.8856 (tt0) cc_final: 0.8339 (tt0) REVERT: G 89 ASN cc_start: 0.9042 (m-40) cc_final: 0.8747 (m-40) REVERT: G 92 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8455 (mt-10) REVERT: H 37 TYR cc_start: 0.9137 (m-80) cc_final: 0.8713 (m-80) REVERT: H 68 ASP cc_start: 0.9128 (t70) cc_final: 0.8862 (t0) REVERT: H 76 GLU cc_start: 0.8613 (mm-30) cc_final: 0.7858 (mm-30) REVERT: H 79 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8040 (ttm110) REVERT: H 93 GLU cc_start: 0.8973 (mp0) cc_final: 0.8607 (mp0) REVERT: L 20 MET cc_start: 0.7239 (mmt) cc_final: 0.6848 (mpp) REVERT: L 42 SER cc_start: 0.8018 (m) cc_final: 0.7813 (p) REVERT: M 1 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.4509 (pmm) outliers start: 14 outliers final: 10 residues processed: 185 average time/residue: 0.2674 time to fit residues: 71.3884 Evaluate side-chains 184 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 1 MET 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 41 optimal weight: 0.9990 chunk 46 optimal weight: 0.0370 chunk 37 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 117 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 0.0770 chunk 90 optimal weight: 7.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN G 38 ASN ** 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 = 0.3678 r_free = 0.3678 target = 0.060876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.041144 restraints weight = 83823.351| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.45 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 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 = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 14574 Z= 0.205 Angle : 0.771 59.179 20964 Z= 0.466 Chirality : 0.035 0.288 2410 Planarity : 0.004 0.055 1663 Dihedral : 29.465 177.523 4255 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.53 % Favored : 97.37 % Rotamer: Outliers : 1.98 % Allowed : 19.70 % Favored : 78.31 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.28), residues: 988 helix: 2.44 (0.21), residues: 642 sheet: -0.69 (0.98), residues: 28 loop : -0.47 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 141 HIS 0.001 0.000 HIS K 75 PHE 0.010 0.001 PHE A 67 TYR 0.019 0.001 TYR D 83 ARG 0.006 0.000 ARG D 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.138 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: A 41 TYR cc_start: 0.6454 (m-80) cc_final: 0.5957 (m-80) REVERT: B 63 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8460 (mt-10) REVERT: C 56 GLU cc_start: 0.8558 (tt0) cc_final: 0.8289 (tt0) REVERT: C 64 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8133 (tm-30) REVERT: C 65 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9189 (mm) REVERT: C 68 ASN cc_start: 0.8449 (m-40) cc_final: 0.7901 (m-40) REVERT: C 95 LYS cc_start: 0.9151 (tptt) cc_final: 0.8817 (tppt) REVERT: D 63 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8259 (m-40) REVERT: D 67 ASN cc_start: 0.9162 (m-40) cc_final: 0.8770 (m110) REVERT: D 68 ASP cc_start: 0.9043 (t70) cc_final: 0.8668 (t0) REVERT: E 94 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8100 (mt-10) REVERT: F 22 LEU cc_start: 0.8162 (pt) cc_final: 0.7910 (tt) REVERT: G 56 GLU cc_start: 0.8867 (tt0) cc_final: 0.8338 (tt0) REVERT: G 89 ASN cc_start: 0.9047 (m-40) cc_final: 0.8748 (m-40) REVERT: G 92 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8468 (mt-10) REVERT: H 37 TYR cc_start: 0.9147 (m-80) cc_final: 0.8703 (m-80) REVERT: H 68 ASP cc_start: 0.9137 (t70) cc_final: 0.8870 (t0) REVERT: H 76 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7863 (mm-30) REVERT: H 79 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.8037 (ttm110) REVERT: H 93 GLU cc_start: 0.8966 (mp0) cc_final: 0.8604 (mp0) REVERT: L 20 MET cc_start: 0.7235 (mmt) cc_final: 0.6841 (mpp) REVERT: L 42 SER cc_start: 0.8022 (m) cc_final: 0.7811 (p) REVERT: M 1 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.4486 (pmm) outliers start: 16 outliers final: 12 residues processed: 178 average time/residue: 0.2540 time to fit residues: 65.9713 Evaluate side-chains 186 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain M residue 1 MET 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 14 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 47 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3666 r_free = 0.3666 target = 0.060276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.040504 restraints weight = 84222.890| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.41 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 14574 Z= 0.284 Angle : 0.765 52.365 20964 Z= 0.464 Chirality : 0.036 0.161 2410 Planarity : 0.004 0.049 1663 Dihedral : 29.432 177.614 4255 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.11 % Allowed : 19.58 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.28), residues: 988 helix: 2.44 (0.21), residues: 642 sheet: -0.68 (0.99), residues: 28 loop : -0.49 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 141 HIS 0.002 0.001 HIS M 68 PHE 0.009 0.001 PHE F 61 TYR 0.023 0.001 TYR D 83 ARG 0.004 0.000 ARG D 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5664.82 seconds wall clock time: 102 minutes 50.52 seconds (6170.52 seconds total)