Starting phenix.real_space_refine on Thu Jun 12 20:17:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7j_38100/06_2025/8x7j_38100.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7j_38100/06_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_38100/06_2025/8x7j_38100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7j_38100/06_2025/8x7j_38100.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7j_38100/06_2025/8x7j_38100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7j_38100/06_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-5710/modules/chem_data/mon_lib" Total number of atoms: 13739 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 642 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2967 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2937 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "K" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1031 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 126} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "L" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 405 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 399 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 56} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13064 SG CYS L 31 59.328 67.509 25.982 1.00218.04 S ATOM 13203 SG CYS L 51 60.840 71.001 26.041 1.00210.14 S ATOM 13227 SG CYS L 54 57.120 70.534 25.078 1.00213.50 S ATOM 12959 SG CYS L 16 71.165 67.606 21.224 1.00283.03 S ATOM 12977 SG CYS L 19 74.736 68.117 20.046 1.00282.47 S ATOM 13100 SG CYS L 36 74.096 65.680 22.767 1.00253.66 S ATOM 13118 SG CYS L 39 73.702 69.387 23.482 1.00248.31 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 75 " occ=0.45 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.45 Time building chain proxies: 8.18, per 1000 atoms: 0.60 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: 3.41 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 33 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 54 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 16 " Number of angles added : 9 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1918 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 13 sheets defined 63.1% alpha, 4.4% beta 143 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 6.41 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: 4.90 Time building geometry restraints manager: 3.77 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: 1.130 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 39.230 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14582 Z= 0.149 Angle : 0.517 5.210 20973 Z= 0.317 Chirality : 0.033 0.131 2410 Planarity : 0.003 0.034 1663 Dihedral : 25.848 178.758 6090 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.73 % Allowed : 4.46 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.12179 ( 823) hydrogen bonds : angle 3.69416 ( 2018) metal coordination : bond 0.00815 ( 8) metal coordination : angle 1.56213 ( 9) covalent geometry : bond 0.00312 (14574) covalent geometry : angle 0.51640 (20964) *********************** 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 : 1.030 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: 0.3309 time to fit residues: 116.9972 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 : 1.001 ------------------------------------------------------------------------------- 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 = 82357.587| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.42 r_work (final): 0.3017 ------------------------------------------------------------------------------- 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 0.042 14582 Z= 0.151 Angle : 0.566 9.157 20973 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 Details of bonding type rmsd hydrogen bonds : bond 0.08483 ( 823) hydrogen bonds : angle 3.12612 ( 2018) metal coordination : bond 0.01929 ( 8) metal coordination : angle 2.18020 ( 9) covalent geometry : bond 0.00317 (14574) covalent geometry : angle 0.56450 (20964) *********************** 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 : 1.220 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: 0.8901 (mp) REVERT: B 88 TYR cc_start: 0.8965 (m-10) cc_final: 0.8349 (m-10) REVERT: C 56 GLU cc_start: 0.8531 (tt0) cc_final: 0.8239 (tt0) REVERT: C 68 ASN cc_start: 0.8653 (m-40) cc_final: 0.8346 (m-40) REVERT: D 51 ASP cc_start: 0.8344 (p0) cc_final: 0.8129 (p0) REVERT: D 67 ASN cc_start: 0.9127 (m-40) cc_final: 0.8856 (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: 0.8847 (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: 0.8219 (mtm-85) cc_final: 0.7834 (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: 0.7922 (p) REVERT: M 1 MET cc_start: 0.7685 (ptt) cc_final: 0.6714 (ppp) outliers start: 18 outliers final: 13 residues processed: 205 average time/residue: 0.2661 time to fit residues: 78.4033 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 : 1.155 ------------------------------------------------------------------------------- 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: 0.9980 chunk 102 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 40 optimal weight: 0.0570 chunk 90 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.5702 ------------------------------------------------------------------------------- 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 H 82 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.060719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.041120 restraints weight = 83531.067| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.39 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 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 = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14582 Z= 0.167 Angle : 0.562 10.151 20973 Z= 0.330 Chirality : 0.035 0.161 2410 Planarity : 0.004 0.047 1663 Dihedral : 29.565 178.424 4262 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.11 % Allowed : 12.39 % Favored : 85.50 % 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: 2.50 (0.28), residues: 988 helix: 2.67 (0.21), residues: 649 sheet: -0.32 (1.05), residues: 28 loop : -0.38 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 141 HIS 0.002 0.001 HIS M 68 PHE 0.007 0.001 PHE E 67 TYR 0.029 0.001 TYR D 83 ARG 0.003 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.07810 ( 823) hydrogen bonds : angle 3.09304 ( 2018) metal coordination : bond 0.00580 ( 8) metal coordination : angle 2.03665 ( 9) covalent geometry : bond 0.00368 (14574) covalent geometry : angle 0.56078 (20964) *********************** 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 201 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8586 (tt0) cc_final: 0.8282 (tt0) REVERT: C 64 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8010 (tm-30) REVERT: C 65 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9283 (mm) REVERT: C 68 ASN cc_start: 0.8689 (m-40) cc_final: 0.8172 (m-40) REVERT: D 68 ASP cc_start: 0.8978 (t70) cc_final: 0.8675 (t0) REVERT: D 93 GLU cc_start: 0.8689 (mp0) cc_final: 0.8442 (mp0) REVERT: E 94 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8269 (mt-10) REVERT: E 133 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7867 (mt-10) REVERT: F 22 LEU cc_start: 0.8162 (pt) cc_final: 0.7894 (tt) REVERT: G 38 ASN cc_start: 0.7395 (t0) cc_final: 0.6948 (t0) REVERT: G 56 GLU cc_start: 0.8838 (tt0) cc_final: 0.8311 (tt0) REVERT: G 92 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8638 (mt-10) REVERT: H 68 ASP cc_start: 0.9138 (t70) cc_final: 0.8796 (t0) REVERT: H 113 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8762 (mt-10) REVERT: K 147 MET cc_start: 0.7817 (mtt) cc_final: 0.6981 (mtt) REVERT: L 42 SER cc_start: 0.7893 (m) cc_final: 0.7691 (p) REVERT: L 61 TRP cc_start: 0.7435 (t60) cc_final: 0.7082 (t60) REVERT: M 1 MET cc_start: 0.7761 (ptt) cc_final: 0.6528 (mtp) REVERT: M 18 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8372 (tm-30) outliers start: 17 outliers final: 11 residues processed: 192 average time/residue: 0.2817 time to fit residues: 78.5735 Evaluate side-chains 186 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 95 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain 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: 0.7980 chunk 106 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.059943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.040142 restraints weight = 83943.802| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.38 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 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 = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 14582 Z= 0.204 Angle : 0.570 8.905 20973 Z= 0.334 Chirality : 0.035 0.141 2410 Planarity : 0.004 0.052 1663 Dihedral : 29.618 177.935 4261 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.97 % Allowed : 12.52 % Favored : 84.51 % 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: 2.66 (0.21), residues: 643 sheet: -0.45 (1.03), residues: 28 loop : -0.45 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 93 HIS 0.003 0.001 HIS M 68 PHE 0.009 0.001 PHE E 67 TYR 0.019 0.001 TYR D 83 ARG 0.008 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.07850 ( 823) hydrogen bonds : angle 3.17197 ( 2018) metal coordination : bond 0.00659 ( 8) metal coordination : angle 2.45163 ( 9) covalent geometry : bond 0.00455 (14574) covalent geometry : angle 0.56770 (20964) *********************** 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 194 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8249 (tp30) cc_final: 0.8046 (tm-30) REVERT: C 56 GLU cc_start: 0.8558 (tt0) cc_final: 0.8257 (tt0) REVERT: C 64 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8030 (tm-30) REVERT: C 65 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9235 (mm) REVERT: C 68 ASN cc_start: 0.8517 (m-40) cc_final: 0.8056 (m-40) REVERT: D 63 ASN cc_start: 0.9282 (OUTLIER) cc_final: 0.8683 (m-40) REVERT: D 68 ASP cc_start: 0.9013 (t70) cc_final: 0.8726 (t0) REVERT: D 93 GLU cc_start: 0.8790 (mp0) cc_final: 0.8428 (mp0) REVERT: E 94 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8202 (mt-10) REVERT: F 22 LEU cc_start: 0.8165 (pt) cc_final: 0.7909 (tt) REVERT: G 38 ASN cc_start: 0.7509 (t0) cc_final: 0.7227 (t0) REVERT: G 56 GLU cc_start: 0.8847 (tt0) cc_final: 0.8335 (tt0) REVERT: G 92 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8541 (mt-10) REVERT: H 37 TYR cc_start: 0.9044 (m-80) cc_final: 0.8465 (m-80) REVERT: H 68 ASP cc_start: 0.9143 (t70) cc_final: 0.8811 (t0) REVERT: H 79 ARG cc_start: 0.8434 (mtm-85) cc_final: 0.7875 (mtm-85) REVERT: H 93 GLU cc_start: 0.8811 (mp0) cc_final: 0.8586 (mp0) REVERT: H 113 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8776 (mt-10) REVERT: K 147 MET cc_start: 0.7827 (mtt) cc_final: 0.7007 (mtt) REVERT: L 42 SER cc_start: 0.7901 (m) cc_final: 0.7696 (p) REVERT: M 1 MET cc_start: 0.7795 (ptt) cc_final: 0.6492 (mtp) REVERT: M 18 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8278 (tm-30) outliers start: 24 outliers final: 18 residues processed: 182 average time/residue: 0.2513 time to fit residues: 66.3055 Evaluate side-chains 183 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain 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 H residue 80 LEU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 33 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 116 optimal weight: 50.0000 chunk 89 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 101 optimal weight: 0.0970 overall best weight: 3.2186 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.059222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.039480 restraints weight = 84551.945| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.35 r_work (final): 0.2930 ------------------------------------------------------------------------------- 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: 0.8454 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 14582 Z= 0.239 Angle : 0.587 8.323 20973 Z= 0.343 Chirality : 0.036 0.157 2410 Planarity : 0.004 0.050 1663 Dihedral : 29.692 177.566 4261 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.10 % Allowed : 13.88 % 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: 2.27 (0.28), residues: 988 helix: 2.54 (0.21), residues: 643 sheet: -0.65 (1.01), residues: 28 loop : -0.50 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 93 HIS 0.004 0.001 HIS M 68 PHE 0.010 0.001 PHE E 67 TYR 0.016 0.002 TYR H 40 ARG 0.004 0.000 ARG K 136 Details of bonding type rmsd hydrogen bonds : bond 0.07912 ( 823) hydrogen bonds : angle 3.29247 ( 2018) metal coordination : bond 0.00623 ( 8) metal coordination : angle 2.80909 ( 9) covalent geometry : bond 0.00533 (14574) covalent geometry : angle 0.58445 (20964) *********************** 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 194 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8548 (tt0) cc_final: 0.8265 (tt0) REVERT: C 64 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8084 (tm-30) REVERT: C 65 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9272 (mm) REVERT: C 68 ASN cc_start: 0.8721 (m-40) cc_final: 0.8149 (m-40) REVERT: D 68 ASP cc_start: 0.9025 (t70) cc_final: 0.8749 (t0) REVERT: F 22 LEU cc_start: 0.8194 (pt) cc_final: 0.7931 (tt) REVERT: G 38 ASN cc_start: 0.7560 (t0) cc_final: 0.7345 (t0) REVERT: G 56 GLU cc_start: 0.8853 (tt0) cc_final: 0.8363 (tt0) REVERT: G 92 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8492 (mt-10) REVERT: H 37 TYR cc_start: 0.9076 (m-80) cc_final: 0.8662 (m-80) REVERT: H 68 ASP cc_start: 0.9143 (t70) cc_final: 0.8861 (t0) REVERT: H 76 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8385 (mm-30) REVERT: H 79 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.7804 (mtm-85) REVERT: H 93 GLU cc_start: 0.8799 (mp0) cc_final: 0.8473 (mp0) REVERT: H 113 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8736 (mt-10) REVERT: K 89 LEU cc_start: 0.9152 (mt) cc_final: 0.8923 (tp) REVERT: K 147 MET cc_start: 0.7643 (mtt) cc_final: 0.6814 (mtt) REVERT: M 1 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.6381 (mtp) REVERT: M 18 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8255 (tm-30) outliers start: 25 outliers final: 18 residues processed: 181 average time/residue: 0.2476 time to fit residues: 65.5404 Evaluate side-chains 182 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 95 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 36 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.059943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.039974 restraints weight = 84436.026| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.43 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: 0.8442 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14582 Z= 0.180 Angle : 0.563 7.736 20973 Z= 0.332 Chirality : 0.035 0.149 2410 Planarity : 0.003 0.049 1663 Dihedral : 29.640 177.828 4261 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.35 % Allowed : 15.37 % Favored : 82.28 % 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: 2.29 (0.28), residues: 988 helix: 2.56 (0.21), residues: 643 sheet: -0.69 (1.01), residues: 28 loop : -0.52 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 93 HIS 0.002 0.001 HIS M 68 PHE 0.011 0.001 PHE E 67 TYR 0.013 0.001 TYR H 40 ARG 0.003 0.000 ARG K 136 Details of bonding type rmsd hydrogen bonds : bond 0.07777 ( 823) hydrogen bonds : angle 3.17917 ( 2018) metal coordination : bond 0.00553 ( 8) metal coordination : angle 2.43061 ( 9) covalent geometry : bond 0.00399 (14574) covalent geometry : angle 0.56126 (20964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7555 (pp20) REVERT: C 56 GLU cc_start: 0.8561 (tt0) cc_final: 0.8265 (tt0) REVERT: C 64 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8151 (tm-30) REVERT: C 65 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9248 (mm) REVERT: D 63 ASN cc_start: 0.9280 (OUTLIER) cc_final: 0.8608 (m-40) REVERT: D 68 ASP cc_start: 0.9020 (t70) cc_final: 0.8740 (t0) REVERT: D 76 GLU cc_start: 0.9099 (tp30) cc_final: 0.8833 (tp30) REVERT: D 79 ARG cc_start: 0.8857 (ttp-110) cc_final: 0.8526 (ttm110) REVERT: E 94 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8113 (mt-10) REVERT: F 22 LEU cc_start: 0.8177 (pt) cc_final: 0.7922 (tt) REVERT: G 38 ASN cc_start: 0.7457 (t0) cc_final: 0.7253 (t0) REVERT: G 56 GLU cc_start: 0.8876 (tt0) cc_final: 0.8362 (tt0) REVERT: G 89 ASN cc_start: 0.9023 (m-40) cc_final: 0.8768 (m-40) REVERT: G 92 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8472 (mt-10) REVERT: H 37 TYR cc_start: 0.9140 (m-80) cc_final: 0.8721 (m-80) REVERT: H 68 ASP cc_start: 0.9155 (t70) cc_final: 0.8877 (t0) REVERT: H 76 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8425 (mm-30) REVERT: H 79 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.7818 (mtm-85) REVERT: K 89 LEU cc_start: 0.9158 (mt) cc_final: 0.8926 (tp) REVERT: K 147 MET cc_start: 0.7615 (mtt) cc_final: 0.6808 (mtt) REVERT: L 20 MET cc_start: 0.7439 (mmt) cc_final: 0.7094 (mpp) REVERT: M 1 MET cc_start: 0.7712 (ptt) cc_final: 0.6529 (mtp) REVERT: M 18 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8359 (tm-30) outliers start: 19 outliers final: 16 residues processed: 182 average time/residue: 0.2496 time to fit residues: 66.5844 Evaluate side-chains 183 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 49 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 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.059398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.039451 restraints weight = 85493.002| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.43 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 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 = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14582 Z= 0.215 Angle : 0.579 7.480 20973 Z= 0.340 Chirality : 0.036 0.159 2410 Planarity : 0.004 0.046 1663 Dihedral : 29.652 177.116 4261 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.60 % Allowed : 16.36 % Favored : 81.04 % 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: 2.25 (0.28), residues: 988 helix: 2.54 (0.21), residues: 643 sheet: -0.74 (1.01), residues: 28 loop : -0.56 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 93 HIS 0.003 0.001 HIS M 68 PHE 0.010 0.001 PHE E 67 TYR 0.047 0.002 TYR D 83 ARG 0.005 0.000 ARG G 88 Details of bonding type rmsd hydrogen bonds : bond 0.07813 ( 823) hydrogen bonds : angle 3.20073 ( 2018) metal coordination : bond 0.00569 ( 8) metal coordination : angle 2.58239 ( 9) covalent geometry : bond 0.00478 (14574) covalent geometry : angle 0.57692 (20964) *********************** 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: 21 poor density : 166 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8565 (tt0) cc_final: 0.8285 (tt0) REVERT: C 64 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8131 (tm-30) REVERT: C 65 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9259 (mm) REVERT: D 35 GLU cc_start: 0.8223 (pp20) cc_final: 0.7980 (pp20) REVERT: D 63 ASN cc_start: 0.9286 (OUTLIER) cc_final: 0.8624 (m-40) REVERT: D 68 ASP cc_start: 0.9059 (t70) cc_final: 0.8790 (t0) REVERT: E 94 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8106 (mt-10) REVERT: F 22 LEU cc_start: 0.8187 (pt) cc_final: 0.7920 (tt) REVERT: G 56 GLU cc_start: 0.8862 (tt0) cc_final: 0.8304 (tt0) REVERT: G 89 ASN cc_start: 0.9028 (m-40) cc_final: 0.8758 (m-40) REVERT: G 92 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8454 (mt-10) REVERT: H 37 TYR cc_start: 0.9148 (m-80) cc_final: 0.8721 (m-80) REVERT: H 68 ASP cc_start: 0.9136 (t70) cc_final: 0.8855 (t0) REVERT: H 79 ARG cc_start: 0.8480 (mtm-85) cc_final: 0.7825 (mtm-85) REVERT: K 147 MET cc_start: 0.7577 (mtt) cc_final: 0.6780 (mtt) REVERT: L 20 MET cc_start: 0.7400 (mmt) cc_final: 0.7094 (mpp) REVERT: M 1 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.6192 (ppp) REVERT: M 18 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8316 (tm-30) outliers start: 21 outliers final: 15 residues processed: 178 average time/residue: 0.2504 time to fit residues: 65.3015 Evaluate side-chains 179 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 115 optimal weight: 0.0470 chunk 112 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.060399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.040647 restraints weight = 83871.378| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.42 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 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 = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14582 Z= 0.154 Angle : 0.564 7.281 20973 Z= 0.332 Chirality : 0.035 0.173 2410 Planarity : 0.004 0.048 1663 Dihedral : 29.540 177.642 4261 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.35 % Allowed : 16.98 % Favored : 80.67 % 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: 2.25 (0.28), residues: 988 helix: 2.55 (0.21), residues: 643 sheet: -0.65 (0.99), residues: 28 loop : -0.57 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 141 HIS 0.003 0.000 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.037 0.001 TYR D 83 ARG 0.006 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.07896 ( 823) hydrogen bonds : angle 3.03925 ( 2018) metal coordination : bond 0.00452 ( 8) metal coordination : angle 1.98613 ( 9) covalent geometry : bond 0.00336 (14574) covalent geometry : angle 0.56303 (20964) *********************** 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 195 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8558 (tt0) cc_final: 0.8267 (tt0) REVERT: C 64 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8163 (tm-30) REVERT: C 65 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9264 (mm) REVERT: C 68 ASN cc_start: 0.8600 (m-40) cc_final: 0.7974 (m-40) REVERT: C 95 LYS cc_start: 0.9192 (tptt) cc_final: 0.8816 (tppt) REVERT: D 63 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8212 (m-40) REVERT: D 67 ASN cc_start: 0.9170 (m-40) cc_final: 0.8799 (m110) REVERT: D 68 ASP cc_start: 0.9035 (t70) cc_final: 0.8664 (t0) REVERT: D 93 GLU cc_start: 0.8830 (mp0) cc_final: 0.8614 (mp0) REVERT: E 94 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8129 (mt-10) REVERT: F 22 LEU cc_start: 0.8178 (pt) cc_final: 0.7938 (tt) REVERT: G 56 GLU cc_start: 0.8863 (tt0) cc_final: 0.8286 (tt0) REVERT: G 89 ASN cc_start: 0.9040 (m-40) cc_final: 0.8747 (m-40) REVERT: G 92 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8456 (mt-10) REVERT: H 37 TYR cc_start: 0.9159 (m-80) cc_final: 0.8755 (m-80) REVERT: H 68 ASP cc_start: 0.9160 (t70) cc_final: 0.8909 (t0) REVERT: H 76 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7576 (mm-30) REVERT: H 79 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8039 (ttm110) REVERT: L 20 MET cc_start: 0.7407 (mmt) cc_final: 0.7075 (mpp) REVERT: M 1 MET cc_start: 0.7842 (ptt) cc_final: 0.6442 (ppp) REVERT: M 18 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8425 (tm-30) outliers start: 19 outliers final: 13 residues processed: 186 average time/residue: 0.2633 time to fit residues: 70.8537 Evaluate side-chains 184 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 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 L residue 51 CYS 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: 0.9980 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.060939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041177 restraints weight = 83223.910| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.43 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 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 = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14582 Z= 0.146 Angle : 0.563 7.534 20973 Z= 0.331 Chirality : 0.034 0.171 2410 Planarity : 0.003 0.047 1663 Dihedral : 29.432 177.416 4259 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.11 % Allowed : 17.60 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.26 (0.28), residues: 988 helix: 2.53 (0.21), residues: 642 sheet: -0.51 (1.00), residues: 28 loop : -0.51 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 141 HIS 0.002 0.000 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.030 0.001 TYR D 83 ARG 0.003 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.07919 ( 823) hydrogen bonds : angle 2.99759 ( 2018) metal coordination : bond 0.00369 ( 8) metal coordination : angle 1.72036 ( 9) covalent geometry : bond 0.00316 (14574) covalent geometry : angle 0.56227 (20964) *********************** 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 195 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8460 (mt-10) REVERT: C 56 GLU cc_start: 0.8559 (tt0) cc_final: 0.8275 (tt0) REVERT: C 64 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8189 (tm-30) REVERT: C 65 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9265 (mm) REVERT: C 68 ASN cc_start: 0.8548 (m-40) cc_final: 0.8044 (m-40) REVERT: C 95 LYS cc_start: 0.9183 (tptt) cc_final: 0.8820 (tppt) REVERT: D 63 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8910 (t0) REVERT: D 68 ASP cc_start: 0.9046 (t70) cc_final: 0.8660 (t0) REVERT: E 94 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8154 (mt-10) REVERT: F 22 LEU cc_start: 0.8176 (pt) cc_final: 0.7937 (tt) REVERT: G 56 GLU cc_start: 0.8858 (tt0) cc_final: 0.8331 (tt0) REVERT: G 89 ASN cc_start: 0.9054 (m-40) cc_final: 0.8752 (m-40) REVERT: G 92 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8449 (mt-10) REVERT: H 37 TYR cc_start: 0.9159 (m-80) cc_final: 0.8736 (m-80) REVERT: H 68 ASP cc_start: 0.9142 (t70) cc_final: 0.8896 (t0) REVERT: H 76 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7686 (mm-30) REVERT: H 79 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8208 (ttm110) REVERT: K 147 MET cc_start: 0.7698 (mtt) cc_final: 0.6895 (mtt) REVERT: M 1 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.6449 (ppp) REVERT: M 18 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8430 (tm-30) outliers start: 17 outliers final: 12 residues processed: 186 average time/residue: 0.2560 time to fit residues: 69.1665 Evaluate side-chains 184 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain 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 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: 0.7980 chunk 46 optimal weight: 0.0270 chunk 37 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 117 optimal weight: 0.0000 chunk 87 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 overall best weight: 1.0844 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.060810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.041267 restraints weight = 83077.536| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.40 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 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 = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14582 Z= 0.154 Angle : 0.568 7.121 20973 Z= 0.333 Chirality : 0.034 0.172 2410 Planarity : 0.003 0.047 1663 Dihedral : 29.400 177.011 4255 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.98 % Allowed : 18.34 % 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: 2.29 (0.28), residues: 988 helix: 2.53 (0.21), residues: 643 sheet: -0.49 (1.00), residues: 28 loop : -0.45 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 141 HIS 0.003 0.000 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.022 0.001 TYR D 83 ARG 0.005 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.07819 ( 823) hydrogen bonds : angle 3.00664 ( 2018) metal coordination : bond 0.00339 ( 8) metal coordination : angle 1.59055 ( 9) covalent geometry : bond 0.00338 (14574) covalent geometry : angle 0.56759 (20964) ********************** 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 189 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6441 (m-80) cc_final: 0.5937 (m-80) REVERT: C 56 GLU cc_start: 0.8557 (tt0) cc_final: 0.8277 (tt0) REVERT: C 64 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8135 (tm-30) REVERT: C 65 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9229 (mm) REVERT: C 68 ASN cc_start: 0.8547 (m-40) cc_final: 0.7970 (m-40) REVERT: C 95 LYS cc_start: 0.9168 (tptt) cc_final: 0.8820 (tppt) REVERT: D 68 ASP cc_start: 0.9060 (t70) cc_final: 0.8677 (t0) REVERT: D 86 ARG cc_start: 0.8624 (mmt90) cc_final: 0.8255 (mtt-85) REVERT: E 94 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8142 (mt-10) REVERT: F 22 LEU cc_start: 0.8167 (pt) cc_final: 0.7922 (tt) REVERT: G 56 GLU cc_start: 0.8851 (tt0) cc_final: 0.8328 (tt0) REVERT: G 89 ASN cc_start: 0.9049 (m-40) cc_final: 0.8747 (m-40) REVERT: G 92 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8462 (mt-10) REVERT: H 37 TYR cc_start: 0.9139 (m-80) cc_final: 0.8608 (m-80) REVERT: H 68 ASP cc_start: 0.9151 (t70) cc_final: 0.8916 (t0) REVERT: H 76 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7679 (mm-30) REVERT: H 79 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8200 (ttm110) REVERT: K 147 MET cc_start: 0.7645 (mtt) cc_final: 0.6818 (mtt) REVERT: L 20 MET cc_start: 0.7208 (mmt) cc_final: 0.6796 (mpp) REVERT: M 1 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6299 (ppp) REVERT: M 18 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8297 (tm-30) outliers start: 16 outliers final: 12 residues processed: 182 average time/residue: 0.2630 time to fit residues: 69.2200 Evaluate side-chains 184 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain 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: 1.9990 chunk 59 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 chunk 117 optimal weight: 40.0000 chunk 26 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 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 = 0.3656 r_free = 0.3656 target = 0.059656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.039855 restraints weight = 85110.129| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.44 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 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 = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14582 Z= 0.219 Angle : 0.606 9.851 20973 Z= 0.352 Chirality : 0.036 0.166 2410 Planarity : 0.004 0.046 1663 Dihedral : 29.517 176.085 4255 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.73 % Allowed : 18.96 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.28), residues: 988 helix: 2.43 (0.21), residues: 644 sheet: -0.61 (1.00), residues: 28 loop : -0.50 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 33 HIS 0.003 0.001 HIS F 75 PHE 0.012 0.001 PHE F 61 TYR 0.025 0.001 TYR D 83 ARG 0.004 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.07838 ( 823) hydrogen bonds : angle 3.18641 ( 2018) metal coordination : bond 0.00499 ( 8) metal coordination : angle 2.29057 ( 9) covalent geometry : bond 0.00491 (14574) covalent geometry : angle 0.60379 (20964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6204.10 seconds wall clock time: 107 minutes 13.02 seconds (6433.02 seconds total)