Starting phenix.real_space_refine on Thu Jun 12 15:20:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7k_38101/06_2025/8x7k_38101.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7k_38101/06_2025/8x7k_38101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x7k_38101/06_2025/8x7k_38101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7k_38101/06_2025/8x7k_38101.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7k_38101/06_2025/8x7k_38101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7k_38101/06_2025/8x7k_38101.cif" } resolution = 3.27 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 1133 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 286 5.49 5 S 24 5.16 5 C 7527 2.51 5 N 2489 2.21 5 O 3059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 13387 Number of models: 1 Model: "" Number of chains: 13 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: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2948 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2915 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1139 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 400 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 31 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 13109 SG CYS L 31 60.059 69.150 26.494 1.00258.38 S ATOM 13259 SG CYS L 51 62.331 72.122 26.337 1.00256.92 S ATOM 13283 SG CYS L 54 58.552 72.626 25.943 1.00257.61 S ATOM 13000 SG CYS L 16 72.742 69.224 21.927 1.00277.18 S ATOM 13018 SG CYS L 19 76.269 68.875 20.741 1.00278.85 S ATOM 13148 SG CYS L 36 75.177 66.760 23.539 1.00279.94 S ATOM 13170 SG CYS L 39 75.610 70.474 24.195 1.00280.00 S Time building chain proxies: 8.08, per 1000 atoms: 0.60 Number of scatterers: 13387 At special positions: 0 Unit cell: (118.14, 125.658, 114.918, 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 24 16.00 P 286 15.00 O 3059 8.00 N 2489 7.00 C 7527 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: 3.65 Conformation dependent library (CDL) restraints added in 1.1 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 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 54 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 16 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 39 " Number of angles added : 9 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 66.0% alpha, 4.4% beta 144 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 6.97 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 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 77 removed outlier: 3.837A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.640A 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: 4.475A 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 103 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.368A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.485A 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: 3.602A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 29 removed outlier: 3.816A pdb=" N ASN F 25 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.964A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.615A 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: 4.538A 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 2 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 146 Processing helix chain 'L' and resid 36 through 44 Processing helix chain 'L' and resid 58 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.777A 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: 7.573A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.644A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.040A 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: 7.361A 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 22 through 25 Processing sheet with id=AB3, first strand: chain 'L' and resid 27 through 28 477 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 4.97 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2956 1.33 - 1.45: 4165 1.45 - 1.57: 6488 1.57 - 1.69: 570 1.69 - 1.81: 38 Bond restraints: 14217 Sorted by residual: bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" C THR E 118 " pdb=" N ILE E 119 " ideal model delta sigma weight residual 1.333 1.321 0.012 1.20e-02 6.94e+03 9.44e-01 bond pdb=" O4' DT J 13 " pdb=" C1' DT J 13 " ideal model delta sigma weight residual 1.414 1.395 0.019 2.00e-02 2.50e+03 9.20e-01 bond pdb=" CB PRO E 66 " pdb=" CG PRO E 66 " ideal model delta sigma weight residual 1.492 1.445 0.047 5.00e-02 4.00e+02 8.84e-01 ... (remaining 14212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 19302 1.10 - 2.20: 954 2.20 - 3.30: 171 3.30 - 4.40: 14 4.40 - 5.50: 8 Bond angle restraints: 20449 Sorted by residual: angle pdb=" N VAL L 44 " pdb=" CA VAL L 44 " pdb=" C VAL L 44 " ideal model delta sigma weight residual 111.62 109.36 2.26 7.90e-01 1.60e+00 8.18e+00 angle pdb=" C THR L 43 " pdb=" N VAL L 44 " pdb=" CA VAL L 44 " ideal model delta sigma weight residual 123.16 120.25 2.91 1.06e+00 8.90e-01 7.55e+00 angle pdb=" N ARG L 55 " pdb=" CA ARG L 55 " pdb=" C ARG L 55 " ideal model delta sigma weight residual 110.80 115.70 -4.90 2.13e+00 2.20e-01 5.30e+00 angle pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sigma weight residual 120.20 123.59 -3.39 1.50e+00 4.44e-01 5.09e+00 angle pdb=" C3' DT J 55 " pdb=" C2' DT J 55 " pdb=" C1' DT J 55 " ideal model delta sigma weight residual 101.60 98.33 3.27 1.50e+00 4.44e-01 4.75e+00 ... (remaining 20444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 6416 33.71 - 67.43: 1389 67.43 - 101.14: 20 101.14 - 134.85: 1 134.85 - 168.57: 2 Dihedral angle restraints: 7828 sinusoidal: 5053 harmonic: 2775 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 28.57 -168.57 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 56.30 163.70 1 3.50e+01 8.16e-04 1.54e+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 87.88 132.12 1 3.50e+01 8.16e-04 1.31e+01 ... (remaining 7825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1439 0.027 - 0.054: 646 0.054 - 0.081: 162 0.081 - 0.108: 63 0.108 - 0.136: 20 Chirality restraints: 2330 Sorted by residual: chirality pdb=" CB VAL L 58 " pdb=" CA VAL L 58 " pdb=" CG1 VAL L 58 " pdb=" CG2 VAL L 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" C3' DT I -59 " pdb=" C4' DT I -59 " pdb=" O3' DT I -59 " pdb=" C2' DT I -59 " both_signs ideal model delta sigma weight residual False -2.66 -2.53 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" P DC I -58 " pdb=" OP1 DC I -58 " pdb=" OP2 DC I -58 " pdb=" O5' DC I -58 " both_signs ideal model delta sigma weight residual True 2.35 -2.47 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 2327 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.023 2.00e-02 2.50e+03 9.60e-03 2.76e+00 pdb=" N9 DG I -35 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO D 103 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO H 103 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.021 5.00e-02 4.00e+02 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 181 2.59 - 3.17: 10898 3.17 - 3.75: 25581 3.75 - 4.32: 32661 4.32 - 4.90: 47725 Nonbonded interactions: 117046 Sorted by model distance: nonbonded pdb=" N2 DG I -21 " pdb=" O2 DC J 21 " model vdw 2.018 2.496 nonbonded pdb=" N2 DG I 46 " pdb=" O2 DC J -46 " model vdw 2.039 2.496 nonbonded pdb=" N2 DG I 56 " pdb=" O2 DC J -56 " model vdw 2.044 2.496 nonbonded pdb=" N2 DG I -56 " pdb=" O2 DC J 56 " model vdw 2.048 2.496 nonbonded pdb=" N2 DG I 0 " pdb=" O2 DC J 0 " model vdw 2.053 2.496 ... (remaining 117041 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 14 or resid 16 through 117)) selection = (chain 'G' and (resid 14 or resid 16 through 117)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 123) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 40.840 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.005 0.047 14225 Z= 0.221 Angle : 0.555 5.498 20458 Z= 0.335 Chirality : 0.035 0.136 2330 Planarity : 0.003 0.041 1602 Dihedral : 26.210 168.568 6032 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.37 % Allowed : 5.24 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.28), residues: 932 helix: 2.88 (0.21), residues: 622 sheet: 0.69 (1.12), residues: 22 loop : 0.05 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 93 HIS 0.004 0.001 HIS L 33 PHE 0.008 0.001 PHE A 67 TYR 0.009 0.001 TYR K 127 ARG 0.002 0.000 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.11132 ( 824) hydrogen bonds : angle 3.96818 ( 2006) metal coordination : bond 0.00950 ( 8) metal coordination : angle 2.56743 ( 9) covalent geometry : bond 0.00480 (14217) covalent geometry : angle 0.55202 (20449) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 262 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7277 (m-80) cc_final: 0.6725 (m-80) REVERT: A 59 GLU cc_start: 0.8455 (pt0) cc_final: 0.8234 (pt0) REVERT: A 94 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8271 (mm-30) REVERT: A 120 MET cc_start: 0.8653 (mtm) cc_final: 0.8444 (mtm) REVERT: B 95 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8278 (mtt90) REVERT: C 56 GLU cc_start: 0.8498 (tt0) cc_final: 0.8188 (tt0) REVERT: C 68 ASN cc_start: 0.8798 (m-40) cc_final: 0.8593 (m-40) REVERT: C 72 ASP cc_start: 0.8517 (m-30) cc_final: 0.8289 (m-30) REVERT: C 76 THR cc_start: 0.9124 (p) cc_final: 0.8765 (t) REVERT: C 90 ASP cc_start: 0.8515 (t70) cc_final: 0.8225 (t0) REVERT: C 92 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8281 (mm-30) REVERT: D 34 LYS cc_start: 0.8509 (ptpt) cc_final: 0.8234 (tptt) REVERT: D 68 ASP cc_start: 0.8926 (t70) cc_final: 0.8613 (t0) REVERT: D 83 TYR cc_start: 0.7991 (m-10) cc_final: 0.7418 (m-80) REVERT: D 105 GLU cc_start: 0.7765 (tp30) cc_final: 0.7329 (tp30) REVERT: D 108 LYS cc_start: 0.8708 (mtpm) cc_final: 0.8399 (ttpt) REVERT: E 54 TYR cc_start: 0.9385 (m-80) cc_final: 0.9059 (m-80) REVERT: F 77 LYS cc_start: 0.9052 (mttt) cc_final: 0.8704 (mtpp) REVERT: G 24 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8386 (mm-40) REVERT: G 39 TYR cc_start: 0.9360 (m-80) cc_final: 0.8503 (m-80) REVERT: G 56 GLU cc_start: 0.8428 (tt0) cc_final: 0.7857 (tt0) REVERT: G 89 ASN cc_start: 0.9128 (m-40) cc_final: 0.8615 (m-40) REVERT: G 92 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8069 (mm-30) REVERT: G 95 LYS cc_start: 0.9367 (ttpt) cc_final: 0.9135 (tttm) REVERT: H 68 ASP cc_start: 0.9073 (t70) cc_final: 0.8834 (t0) REVERT: H 83 TYR cc_start: 0.8059 (m-10) cc_final: 0.7416 (m-80) REVERT: H 121 TYR cc_start: 0.8988 (t80) cc_final: 0.8786 (t80) REVERT: K 34 GLN cc_start: 0.8745 (tt0) cc_final: 0.8241 (tm-30) REVERT: K 45 TYR cc_start: 0.6101 (m-80) cc_final: 0.5551 (m-80) REVERT: K 51 PHE cc_start: 0.9296 (m-80) cc_final: 0.9050 (m-80) REVERT: K 87 ASP cc_start: 0.8350 (p0) cc_final: 0.8107 (p0) REVERT: K 117 ASP cc_start: 0.6617 (t0) cc_final: 0.6283 (p0) REVERT: K 143 GLN cc_start: 0.8645 (mt0) cc_final: 0.8297 (mp10) REVERT: L 29 LEU cc_start: 0.7001 (mt) cc_final: 0.6753 (tp) REVERT: L 43 THR cc_start: 0.7501 (t) cc_final: 0.6975 (t) REVERT: L 46 LYS cc_start: 0.9219 (mtmt) cc_final: 0.8731 (ptpt) outliers start: 19 outliers final: 3 residues processed: 274 average time/residue: 0.3644 time to fit residues: 129.9568 Evaluate side-chains 197 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 193 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 95 ARG Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN C 24 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS G 38 ASN G 68 ASN G 104 GLN K 7 ASN L 41 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.074770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046803 restraints weight = 60256.659| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.84 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14225 Z= 0.191 Angle : 0.583 6.926 20458 Z= 0.340 Chirality : 0.036 0.176 2330 Planarity : 0.005 0.066 1602 Dihedral : 30.143 169.507 4186 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.87 % Allowed : 11.36 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.27), residues: 932 helix: 2.81 (0.20), residues: 626 sheet: 0.51 (1.08), residues: 22 loop : -0.11 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 93 HIS 0.004 0.001 HIS L 33 PHE 0.013 0.002 PHE L 40 TYR 0.030 0.002 TYR K 74 ARG 0.007 0.001 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.08101 ( 824) hydrogen bonds : angle 3.38469 ( 2006) metal coordination : bond 0.01585 ( 8) metal coordination : angle 4.45265 ( 9) covalent geometry : bond 0.00421 (14217) covalent geometry : angle 0.57589 (20449) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7047 (m-80) cc_final: 0.6537 (m-80) REVERT: A 120 MET cc_start: 0.8602 (mtm) cc_final: 0.8328 (mtm) REVERT: B 88 TYR cc_start: 0.8847 (m-10) cc_final: 0.7586 (m-10) REVERT: C 56 GLU cc_start: 0.8275 (tt0) cc_final: 0.7926 (tt0) REVERT: C 68 ASN cc_start: 0.8740 (m-40) cc_final: 0.8529 (m-40) REVERT: C 76 THR cc_start: 0.9141 (p) cc_final: 0.8788 (t) REVERT: C 90 ASP cc_start: 0.8698 (t70) cc_final: 0.8429 (t70) REVERT: D 34 LYS cc_start: 0.8505 (ptpt) cc_final: 0.8185 (tptt) REVERT: D 68 ASP cc_start: 0.8931 (t70) cc_final: 0.8717 (t0) REVERT: D 71 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8267 (mm-30) REVERT: D 83 TYR cc_start: 0.7966 (m-10) cc_final: 0.7539 (m-80) REVERT: D 105 GLU cc_start: 0.7755 (tp30) cc_final: 0.7381 (tp30) REVERT: E 54 TYR cc_start: 0.9359 (m-80) cc_final: 0.9069 (m-80) REVERT: E 76 GLN cc_start: 0.8271 (pp30) cc_final: 0.8063 (pp30) REVERT: F 77 LYS cc_start: 0.9105 (mttt) cc_final: 0.8774 (mtpp) REVERT: G 24 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8413 (mp10) REVERT: G 56 GLU cc_start: 0.8594 (tt0) cc_final: 0.8094 (tt0) REVERT: G 89 ASN cc_start: 0.9160 (m-40) cc_final: 0.8705 (m-40) REVERT: G 92 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8160 (mm-30) REVERT: G 95 LYS cc_start: 0.9351 (ttpt) cc_final: 0.9127 (tttm) REVERT: H 83 TYR cc_start: 0.7934 (m-10) cc_final: 0.7549 (m-80) REVERT: H 121 TYR cc_start: 0.9017 (t80) cc_final: 0.8813 (t80) REVERT: K 34 GLN cc_start: 0.8531 (tt0) cc_final: 0.7927 (tm-30) REVERT: K 87 ASP cc_start: 0.8929 (p0) cc_final: 0.8458 (t0) REVERT: K 143 GLN cc_start: 0.8854 (mt0) cc_final: 0.8596 (pt0) REVERT: K 147 MET cc_start: 0.7731 (mtt) cc_final: 0.7486 (mpp) REVERT: L 43 THR cc_start: 0.7391 (t) cc_final: 0.6973 (t) outliers start: 15 outliers final: 11 residues processed: 213 average time/residue: 0.4031 time to fit residues: 118.8750 Evaluate side-chains 197 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 9 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 92 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 105 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.074235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.046317 restraints weight = 60822.969| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.74 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14225 Z= 0.229 Angle : 0.598 10.915 20458 Z= 0.347 Chirality : 0.036 0.154 2330 Planarity : 0.004 0.041 1602 Dihedral : 30.131 170.117 4182 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.75 % Allowed : 11.99 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.27), residues: 932 helix: 2.74 (0.20), residues: 627 sheet: 0.64 (1.03), residues: 22 loop : -0.25 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 33 HIS 0.003 0.001 HIS K 75 PHE 0.012 0.002 PHE A 67 TYR 0.016 0.001 TYR K 74 ARG 0.005 0.001 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.07957 ( 824) hydrogen bonds : angle 3.36509 ( 2006) metal coordination : bond 0.00965 ( 8) metal coordination : angle 4.29293 ( 9) covalent geometry : bond 0.00515 (14217) covalent geometry : angle 0.59090 (20449) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7099 (m-80) cc_final: 0.6653 (m-80) REVERT: A 120 MET cc_start: 0.8618 (mtm) cc_final: 0.8349 (mtm) REVERT: C 56 GLU cc_start: 0.8310 (tt0) cc_final: 0.7946 (tt0) REVERT: C 90 ASP cc_start: 0.8736 (t70) cc_final: 0.8474 (t70) REVERT: D 34 LYS cc_start: 0.8494 (ptpt) cc_final: 0.8096 (tptt) REVERT: D 68 ASP cc_start: 0.8938 (t70) cc_final: 0.8708 (t0) REVERT: D 71 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8251 (mm-30) REVERT: D 83 TYR cc_start: 0.7949 (m-10) cc_final: 0.7370 (m-80) REVERT: E 54 TYR cc_start: 0.9366 (m-80) cc_final: 0.9039 (m-80) REVERT: E 76 GLN cc_start: 0.8450 (pp30) cc_final: 0.8208 (pp30) REVERT: F 77 LYS cc_start: 0.9132 (mttt) cc_final: 0.8811 (mtpp) REVERT: G 24 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8551 (mp10) REVERT: G 56 GLU cc_start: 0.8591 (tt0) cc_final: 0.8085 (tt0) REVERT: G 89 ASN cc_start: 0.9234 (m-40) cc_final: 0.8690 (m-40) REVERT: G 92 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8112 (mm-30) REVERT: G 95 LYS cc_start: 0.9352 (ttpt) cc_final: 0.9122 (tttm) REVERT: H 83 TYR cc_start: 0.7926 (m-10) cc_final: 0.7609 (m-80) REVERT: H 121 TYR cc_start: 0.9035 (t80) cc_final: 0.8817 (t80) REVERT: K 34 GLN cc_start: 0.8635 (tt0) cc_final: 0.8357 (tp40) REVERT: K 92 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8390 (mp10) REVERT: K 147 MET cc_start: 0.8381 (mtt) cc_final: 0.7918 (mpp) REVERT: L 43 THR cc_start: 0.7425 (t) cc_final: 0.6960 (t) outliers start: 22 outliers final: 12 residues processed: 201 average time/residue: 0.3607 time to fit residues: 100.3065 Evaluate side-chains 192 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain L residue 35 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** 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 = 0.3787 r_free = 0.3787 target = 0.075080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.047316 restraints weight = 60087.939| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.79 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14225 Z= 0.162 Angle : 0.576 10.939 20458 Z= 0.336 Chirality : 0.035 0.151 2330 Planarity : 0.004 0.039 1602 Dihedral : 30.018 171.455 4182 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.87 % Allowed : 13.86 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.28), residues: 932 helix: 2.83 (0.20), residues: 631 sheet: 0.46 (1.00), residues: 24 loop : -0.17 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 33 HIS 0.002 0.001 HIS F 75 PHE 0.013 0.001 PHE A 67 TYR 0.007 0.001 TYR K 74 ARG 0.005 0.000 ARG K 136 Details of bonding type rmsd hydrogen bonds : bond 0.07881 ( 824) hydrogen bonds : angle 3.16973 ( 2006) metal coordination : bond 0.00751 ( 8) metal coordination : angle 3.57455 ( 9) covalent geometry : bond 0.00356 (14217) covalent geometry : angle 0.57158 (20449) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8513 (mtm) cc_final: 0.8201 (mtm) REVERT: B 88 TYR cc_start: 0.8829 (m-10) cc_final: 0.7661 (m-10) REVERT: C 56 GLU cc_start: 0.8266 (tt0) cc_final: 0.7906 (tt0) REVERT: C 90 ASP cc_start: 0.8716 (t70) cc_final: 0.8409 (t70) REVERT: D 34 LYS cc_start: 0.8441 (ptpt) cc_final: 0.8057 (tptt) REVERT: D 68 ASP cc_start: 0.8923 (t70) cc_final: 0.8706 (t0) REVERT: D 71 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8256 (mm-30) REVERT: D 83 TYR cc_start: 0.7936 (m-10) cc_final: 0.7598 (m-10) REVERT: E 54 TYR cc_start: 0.9355 (m-80) cc_final: 0.9005 (m-80) REVERT: E 76 GLN cc_start: 0.8486 (pp30) cc_final: 0.8207 (pp30) REVERT: F 77 LYS cc_start: 0.9144 (mttt) cc_final: 0.8832 (mtpp) REVERT: G 24 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8534 (mp10) REVERT: G 56 GLU cc_start: 0.8573 (tt0) cc_final: 0.8060 (tt0) REVERT: G 89 ASN cc_start: 0.9231 (m-40) cc_final: 0.8724 (m-40) REVERT: G 92 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8109 (mm-30) REVERT: G 95 LYS cc_start: 0.9351 (ttpt) cc_final: 0.9105 (tttm) REVERT: H 83 TYR cc_start: 0.7876 (m-10) cc_final: 0.7573 (m-10) REVERT: H 121 TYR cc_start: 0.9047 (t80) cc_final: 0.8836 (t80) REVERT: K 1 MET cc_start: 0.5502 (mmt) cc_final: 0.5204 (tpp) REVERT: K 34 GLN cc_start: 0.8726 (tt0) cc_final: 0.8484 (tp40) REVERT: K 38 MET cc_start: 0.7988 (mpp) cc_final: 0.7375 (tmm) REVERT: K 147 MET cc_start: 0.8227 (mtt) cc_final: 0.7653 (mpp) REVERT: L 43 THR cc_start: 0.7271 (t) cc_final: 0.6796 (t) outliers start: 15 outliers final: 9 residues processed: 208 average time/residue: 0.2952 time to fit residues: 84.7328 Evaluate side-chains 196 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 187 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain L residue 35 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 GLN L 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.074747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.047014 restraints weight = 60507.630| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.77 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14225 Z= 0.186 Angle : 0.589 10.906 20458 Z= 0.342 Chirality : 0.036 0.171 2330 Planarity : 0.004 0.039 1602 Dihedral : 30.032 171.857 4180 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.87 % Allowed : 15.61 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.28), residues: 932 helix: 2.82 (0.20), residues: 632 sheet: 0.55 (0.99), residues: 24 loop : -0.15 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 33 HIS 0.003 0.001 HIS C 31 PHE 0.020 0.001 PHE K 62 TYR 0.026 0.001 TYR K 74 ARG 0.006 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.07801 ( 824) hydrogen bonds : angle 3.17781 ( 2006) metal coordination : bond 0.00867 ( 8) metal coordination : angle 3.48517 ( 9) covalent geometry : bond 0.00416 (14217) covalent geometry : angle 0.58488 (20449) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8540 (mtm) cc_final: 0.8233 (mtm) REVERT: C 56 GLU cc_start: 0.8270 (tt0) cc_final: 0.7914 (tt0) REVERT: C 90 ASP cc_start: 0.8729 (t70) cc_final: 0.8382 (t70) REVERT: D 34 LYS cc_start: 0.8436 (ptpt) cc_final: 0.8048 (tptt) REVERT: D 68 ASP cc_start: 0.8940 (t70) cc_final: 0.8716 (t0) REVERT: D 83 TYR cc_start: 0.7952 (m-10) cc_final: 0.7566 (m-10) REVERT: E 54 TYR cc_start: 0.9351 (m-80) cc_final: 0.8983 (m-80) REVERT: E 76 GLN cc_start: 0.8536 (pp30) cc_final: 0.8235 (pp30) REVERT: F 77 LYS cc_start: 0.9165 (mttt) cc_final: 0.8851 (mtpp) REVERT: F 88 TYR cc_start: 0.9015 (m-10) cc_final: 0.7733 (m-10) REVERT: G 56 GLU cc_start: 0.8580 (tt0) cc_final: 0.7977 (tt0) REVERT: G 89 ASN cc_start: 0.9247 (m-40) cc_final: 0.8693 (m-40) REVERT: G 92 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8117 (mm-30) REVERT: G 95 LYS cc_start: 0.9346 (ttpt) cc_final: 0.9098 (tttm) REVERT: H 83 TYR cc_start: 0.7877 (m-10) cc_final: 0.7671 (m-80) REVERT: H 121 TYR cc_start: 0.9067 (t80) cc_final: 0.8851 (t80) REVERT: K 1 MET cc_start: 0.5979 (mmt) cc_final: 0.5674 (tpp) REVERT: K 34 GLN cc_start: 0.8723 (tt0) cc_final: 0.8491 (tp40) REVERT: K 38 MET cc_start: 0.8032 (mpp) cc_final: 0.7485 (tmm) REVERT: K 147 MET cc_start: 0.8141 (mtt) cc_final: 0.7494 (mpp) REVERT: L 43 THR cc_start: 0.7317 (t) cc_final: 0.6887 (t) outliers start: 15 outliers final: 10 residues processed: 199 average time/residue: 0.2806 time to fit residues: 77.4343 Evaluate side-chains 195 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 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 A residue 124 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 35 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 56 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 GLN L 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.075776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.048108 restraints weight = 60911.022| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.80 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14225 Z= 0.149 Angle : 0.579 10.515 20458 Z= 0.336 Chirality : 0.035 0.179 2330 Planarity : 0.004 0.043 1602 Dihedral : 29.921 173.171 4180 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.12 % Allowed : 16.48 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.28), residues: 932 helix: 2.91 (0.20), residues: 630 sheet: 0.60 (1.01), residues: 24 loop : -0.15 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 33 HIS 0.003 0.001 HIS C 31 PHE 0.013 0.001 PHE A 67 TYR 0.022 0.001 TYR K 74 ARG 0.008 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.07943 ( 824) hydrogen bonds : angle 3.01883 ( 2006) metal coordination : bond 0.00794 ( 8) metal coordination : angle 3.63619 ( 9) covalent geometry : bond 0.00324 (14217) covalent geometry : angle 0.57442 (20449) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 206 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6750 (m-80) cc_final: 0.6159 (m-80) REVERT: A 73 GLU cc_start: 0.8312 (tt0) cc_final: 0.8008 (tt0) REVERT: A 76 GLN cc_start: 0.8831 (tt0) cc_final: 0.8612 (tt0) REVERT: B 88 TYR cc_start: 0.8762 (m-10) cc_final: 0.7283 (m-10) REVERT: B 96 THR cc_start: 0.9290 (m) cc_final: 0.9062 (p) REVERT: C 56 GLU cc_start: 0.8248 (tt0) cc_final: 0.7896 (tt0) REVERT: C 90 ASP cc_start: 0.8671 (t70) cc_final: 0.8327 (t70) REVERT: C 92 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8163 (mm-30) REVERT: D 34 LYS cc_start: 0.8441 (ptpt) cc_final: 0.8059 (tptt) REVERT: D 68 ASP cc_start: 0.8905 (t70) cc_final: 0.8595 (t0) REVERT: D 83 TYR cc_start: 0.7894 (m-10) cc_final: 0.7651 (m-10) REVERT: D 105 GLU cc_start: 0.7761 (tp30) cc_final: 0.7490 (tp30) REVERT: E 54 TYR cc_start: 0.9342 (m-80) cc_final: 0.8951 (m-80) REVERT: E 76 GLN cc_start: 0.8597 (pp30) cc_final: 0.8289 (pp30) REVERT: F 77 LYS cc_start: 0.9166 (mttt) cc_final: 0.8948 (mtpp) REVERT: G 56 GLU cc_start: 0.8560 (tt0) cc_final: 0.8010 (tt0) REVERT: G 89 ASN cc_start: 0.9246 (m-40) cc_final: 0.8762 (m-40) REVERT: G 90 ASP cc_start: 0.8391 (t70) cc_final: 0.8170 (t70) REVERT: G 92 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8164 (mm-30) REVERT: G 95 LYS cc_start: 0.9342 (ttpt) cc_final: 0.9092 (tttm) REVERT: H 68 ASP cc_start: 0.9000 (t0) cc_final: 0.8745 (t0) REVERT: H 72 ARG cc_start: 0.9059 (mtt180) cc_final: 0.8849 (mtt180) REVERT: H 83 TYR cc_start: 0.7867 (m-10) cc_final: 0.7570 (m-10) REVERT: H 121 TYR cc_start: 0.9067 (t80) cc_final: 0.8858 (t80) REVERT: K 1 MET cc_start: 0.5772 (mmt) cc_final: 0.5425 (tpp) REVERT: K 34 GLN cc_start: 0.8685 (tt0) cc_final: 0.8481 (tp40) REVERT: K 38 MET cc_start: 0.7990 (mpp) cc_final: 0.7459 (tmm) REVERT: K 62 PHE cc_start: 0.8637 (m-10) cc_final: 0.8361 (m-10) REVERT: L 40 PHE cc_start: 0.8634 (t80) cc_final: 0.8313 (t80) REVERT: L 43 THR cc_start: 0.7194 (t) cc_final: 0.6560 (t) outliers start: 9 outliers final: 7 residues processed: 210 average time/residue: 0.3221 time to fit residues: 95.2018 Evaluate side-chains 198 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 14 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** 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 = 0.3773 r_free = 0.3773 target = 0.074281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.046740 restraints weight = 60556.977| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.67 r_work: 0.2691 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14225 Z= 0.235 Angle : 0.618 11.364 20458 Z= 0.351 Chirality : 0.037 0.178 2330 Planarity : 0.004 0.038 1602 Dihedral : 30.076 172.336 4180 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.75 % Allowed : 16.48 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.28), residues: 932 helix: 2.76 (0.20), residues: 633 sheet: 0.69 (1.01), residues: 24 loop : -0.11 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 141 HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.019 0.001 TYR K 74 ARG 0.006 0.001 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.07899 ( 824) hydrogen bonds : angle 3.24771 ( 2006) metal coordination : bond 0.01178 ( 8) metal coordination : angle 5.64585 ( 9) covalent geometry : bond 0.00529 (14217) covalent geometry : angle 0.60641 (20449) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7152 (m-80) cc_final: 0.6520 (m-80) REVERT: B 88 TYR cc_start: 0.9159 (m-10) cc_final: 0.8207 (m-10) REVERT: C 56 GLU cc_start: 0.8967 (tt0) cc_final: 0.8634 (tt0) REVERT: C 90 ASP cc_start: 0.8946 (t70) cc_final: 0.8685 (t70) REVERT: D 34 LYS cc_start: 0.8412 (ptpt) cc_final: 0.8018 (tptt) REVERT: D 68 ASP cc_start: 0.9234 (t70) cc_final: 0.9017 (t0) REVERT: D 83 TYR cc_start: 0.8189 (m-10) cc_final: 0.7840 (m-10) REVERT: E 50 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8942 (mt-10) REVERT: F 77 LYS cc_start: 0.9309 (mttt) cc_final: 0.9097 (mtpp) REVERT: F 88 TYR cc_start: 0.9258 (m-10) cc_final: 0.8122 (m-10) REVERT: G 56 GLU cc_start: 0.9121 (tt0) cc_final: 0.8655 (tt0) REVERT: G 89 ASN cc_start: 0.9321 (m-40) cc_final: 0.8824 (m-40) REVERT: G 92 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8142 (mm-30) REVERT: G 95 LYS cc_start: 0.9440 (ttpt) cc_final: 0.9185 (tttm) REVERT: H 83 TYR cc_start: 0.8000 (m-10) cc_final: 0.7759 (m-80) REVERT: H 121 TYR cc_start: 0.9085 (t80) cc_final: 0.8874 (t80) REVERT: K 1 MET cc_start: 0.6270 (mmt) cc_final: 0.5903 (tpp) REVERT: K 34 GLN cc_start: 0.8859 (tt0) cc_final: 0.8549 (tp40) REVERT: L 40 PHE cc_start: 0.8658 (t80) cc_final: 0.8436 (t80) REVERT: L 43 THR cc_start: 0.7190 (t) cc_final: 0.6720 (t) outliers start: 14 outliers final: 10 residues processed: 197 average time/residue: 0.2868 time to fit residues: 77.6822 Evaluate side-chains 190 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 35 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.075593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047871 restraints weight = 61008.435| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.81 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14225 Z= 0.151 Angle : 0.595 10.317 20458 Z= 0.340 Chirality : 0.035 0.173 2330 Planarity : 0.004 0.039 1602 Dihedral : 29.964 173.811 4180 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.12 % Allowed : 17.48 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.28), residues: 932 helix: 2.86 (0.20), residues: 632 sheet: 0.68 (1.01), residues: 24 loop : -0.10 (0.36), residues: 276 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 0.013 0.001 PHE A 67 TYR 0.018 0.001 TYR K 74 ARG 0.009 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.07930 ( 824) hydrogen bonds : angle 3.02030 ( 2006) metal coordination : bond 0.00730 ( 8) metal coordination : angle 4.52682 ( 9) covalent geometry : bond 0.00334 (14217) covalent geometry : angle 0.58724 (20449) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6761 (m-80) cc_final: 0.6328 (m-80) REVERT: B 96 THR cc_start: 0.9295 (m) cc_final: 0.9051 (p) REVERT: C 56 GLU cc_start: 0.8225 (tt0) cc_final: 0.7871 (tt0) REVERT: C 90 ASP cc_start: 0.8719 (t70) cc_final: 0.8374 (t70) REVERT: D 34 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8071 (tptt) REVERT: D 68 ASP cc_start: 0.8925 (t70) cc_final: 0.8711 (t0) REVERT: D 83 TYR cc_start: 0.7857 (m-10) cc_final: 0.7600 (m-10) REVERT: E 54 TYR cc_start: 0.9336 (m-80) cc_final: 0.8915 (m-80) REVERT: F 77 LYS cc_start: 0.9171 (mttt) cc_final: 0.8949 (mtpp) REVERT: F 88 TYR cc_start: 0.8987 (m-10) cc_final: 0.7865 (m-10) REVERT: G 56 GLU cc_start: 0.8567 (tt0) cc_final: 0.8016 (tt0) REVERT: G 89 ASN cc_start: 0.9249 (m-40) cc_final: 0.8745 (m-40) REVERT: G 92 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8202 (mm-30) REVERT: G 95 LYS cc_start: 0.9348 (ttpt) cc_final: 0.9118 (tttm) REVERT: H 83 TYR cc_start: 0.7838 (m-10) cc_final: 0.7523 (m-10) REVERT: H 121 TYR cc_start: 0.9024 (t80) cc_final: 0.8802 (t80) REVERT: K 1 MET cc_start: 0.6145 (mmt) cc_final: 0.5734 (tpp) REVERT: K 34 GLN cc_start: 0.8658 (tt0) cc_final: 0.8433 (tp40) REVERT: L 43 THR cc_start: 0.7019 (t) cc_final: 0.6657 (t) outliers start: 9 outliers final: 9 residues processed: 196 average time/residue: 0.3182 time to fit residues: 86.9242 Evaluate side-chains 194 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 35 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 103 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.075366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.048230 restraints weight = 59762.668| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.74 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14225 Z= 0.161 Angle : 0.610 10.753 20458 Z= 0.345 Chirality : 0.035 0.181 2330 Planarity : 0.004 0.039 1602 Dihedral : 29.933 174.343 4180 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.00 % Allowed : 18.60 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.28), residues: 932 helix: 2.85 (0.20), residues: 632 sheet: 0.70 (1.01), residues: 24 loop : -0.13 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 141 HIS 0.002 0.000 HIS F 75 PHE 0.013 0.001 PHE A 67 TYR 0.021 0.001 TYR K 74 ARG 0.012 0.000 ARG K 136 Details of bonding type rmsd hydrogen bonds : bond 0.07785 ( 824) hydrogen bonds : angle 2.99351 ( 2006) metal coordination : bond 0.00612 ( 8) metal coordination : angle 3.97617 ( 9) covalent geometry : bond 0.00359 (14217) covalent geometry : angle 0.60425 (20449) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6738 (m-80) cc_final: 0.6271 (m-80) REVERT: B 88 TYR cc_start: 0.8763 (m-10) cc_final: 0.7347 (m-10) REVERT: B 96 THR cc_start: 0.9286 (m) cc_final: 0.9047 (p) REVERT: C 56 GLU cc_start: 0.8254 (tt0) cc_final: 0.7892 (tt0) REVERT: C 90 ASP cc_start: 0.8736 (t70) cc_final: 0.8388 (t70) REVERT: D 34 LYS cc_start: 0.8429 (ptpt) cc_final: 0.8063 (tptt) REVERT: D 68 ASP cc_start: 0.8939 (t70) cc_final: 0.8724 (t0) REVERT: E 54 TYR cc_start: 0.9341 (m-80) cc_final: 0.8909 (m-80) REVERT: F 77 LYS cc_start: 0.9165 (mttt) cc_final: 0.8953 (mtpp) REVERT: F 88 TYR cc_start: 0.9001 (m-10) cc_final: 0.7625 (m-10) REVERT: G 56 GLU cc_start: 0.8578 (tt0) cc_final: 0.8019 (tt0) REVERT: G 89 ASN cc_start: 0.9254 (m-40) cc_final: 0.8752 (m-40) REVERT: G 92 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8192 (mm-30) REVERT: G 95 LYS cc_start: 0.9341 (ttpt) cc_final: 0.9115 (tttm) REVERT: H 121 TYR cc_start: 0.9029 (t80) cc_final: 0.8802 (t80) REVERT: K 1 MET cc_start: 0.6155 (mmt) cc_final: 0.5721 (tpp) REVERT: K 34 GLN cc_start: 0.8601 (tt0) cc_final: 0.8385 (tp40) REVERT: L 41 GLN cc_start: 0.7388 (mt0) cc_final: 0.7160 (pt0) REVERT: L 43 THR cc_start: 0.7190 (t) cc_final: 0.6795 (t) outliers start: 8 outliers final: 7 residues processed: 195 average time/residue: 0.4146 time to fit residues: 113.8646 Evaluate side-chains 194 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 18 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 113 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 = 0.3806 r_free = 0.3806 target = 0.075830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048546 restraints weight = 60427.567| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.77 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14225 Z= 0.155 Angle : 0.620 12.960 20458 Z= 0.348 Chirality : 0.035 0.181 2330 Planarity : 0.004 0.041 1602 Dihedral : 29.893 174.844 4180 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.00 % Allowed : 19.10 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.27), residues: 932 helix: 2.77 (0.20), residues: 631 sheet: 0.78 (1.01), residues: 24 loop : -0.12 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 141 HIS 0.002 0.000 HIS F 75 PHE 0.015 0.001 PHE L 40 TYR 0.028 0.002 TYR D 83 ARG 0.011 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.07866 ( 824) hydrogen bonds : angle 3.02386 ( 2006) metal coordination : bond 0.00552 ( 8) metal coordination : angle 4.47419 ( 9) covalent geometry : bond 0.00344 (14217) covalent geometry : angle 0.61334 (20449) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6714 (m-80) cc_final: 0.6308 (m-80) REVERT: B 88 TYR cc_start: 0.8124 (m-10) cc_final: 0.7778 (m-10) REVERT: C 56 GLU cc_start: 0.8206 (tt0) cc_final: 0.7859 (tt0) REVERT: C 90 ASP cc_start: 0.8763 (t70) cc_final: 0.8425 (t70) REVERT: C 92 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8070 (mm-30) REVERT: D 34 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8033 (tptt) REVERT: D 68 ASP cc_start: 0.8922 (t70) cc_final: 0.8719 (t0) REVERT: D 83 TYR cc_start: 0.7911 (m-10) cc_final: 0.7351 (m-80) REVERT: D 105 GLU cc_start: 0.7743 (tp30) cc_final: 0.7486 (tp30) REVERT: E 54 TYR cc_start: 0.9334 (m-80) cc_final: 0.8906 (m-80) REVERT: F 77 LYS cc_start: 0.9160 (mttt) cc_final: 0.8949 (mtpp) REVERT: F 88 TYR cc_start: 0.8381 (m-10) cc_final: 0.8078 (m-10) REVERT: G 56 GLU cc_start: 0.8567 (tt0) cc_final: 0.8014 (tt0) REVERT: G 89 ASN cc_start: 0.9245 (m-40) cc_final: 0.8759 (m-40) REVERT: G 92 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8184 (mm-30) REVERT: G 95 LYS cc_start: 0.9345 (ttpt) cc_final: 0.9118 (tttm) REVERT: H 83 TYR cc_start: 0.7944 (m-80) cc_final: 0.6590 (m-80) REVERT: H 121 TYR cc_start: 0.9021 (t80) cc_final: 0.8792 (t80) REVERT: K 1 MET cc_start: 0.6024 (mmt) cc_final: 0.5586 (tpp) REVERT: K 34 GLN cc_start: 0.8625 (tt0) cc_final: 0.8401 (tp40) REVERT: K 45 TYR cc_start: 0.5727 (m-80) cc_final: 0.5293 (m-80) REVERT: L 40 PHE cc_start: 0.8684 (t80) cc_final: 0.8381 (m-80) REVERT: L 41 GLN cc_start: 0.7379 (mt0) cc_final: 0.7077 (pt0) REVERT: L 43 THR cc_start: 0.7156 (t) cc_final: 0.6750 (t) outliers start: 8 outliers final: 8 residues processed: 195 average time/residue: 0.3409 time to fit residues: 91.9947 Evaluate side-chains 197 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 189 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 18 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 9 optimal weight: 0.0030 chunk 89 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 2 optimal weight: 0.0470 overall best weight: 0.9490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 113 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 = 0.3812 r_free = 0.3812 target = 0.075808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.048571 restraints weight = 60320.326| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.76 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14225 Z= 0.157 Angle : 0.615 12.919 20458 Z= 0.346 Chirality : 0.035 0.182 2330 Planarity : 0.004 0.039 1602 Dihedral : 29.871 175.361 4180 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.12 % Allowed : 18.98 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.27), residues: 932 helix: 2.74 (0.20), residues: 631 sheet: 0.74 (1.02), residues: 24 loop : -0.15 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 33 HIS 0.002 0.000 HIS F 75 PHE 0.020 0.001 PHE K 62 TYR 0.020 0.002 TYR K 74 ARG 0.007 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.07835 ( 824) hydrogen bonds : angle 2.98155 ( 2006) metal coordination : bond 0.00522 ( 8) metal coordination : angle 3.71744 ( 9) covalent geometry : bond 0.00350 (14217) covalent geometry : angle 0.60995 (20449) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6515.01 seconds wall clock time: 116 minutes 45.14 seconds (7005.14 seconds total)