Starting phenix.real_space_refine on Wed Feb 4 07:59:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3k_46536/02_2026/9d3k_46536.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3k_46536/02_2026/9d3k_46536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d3k_46536/02_2026/9d3k_46536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3k_46536/02_2026/9d3k_46536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3k_46536/02_2026/9d3k_46536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3k_46536/02_2026/9d3k_46536.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians P 188 5.49 5 S 14 5.16 5 C 5499 2.51 5 N 1808 2.21 5 O 2169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9678 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 768 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 91} 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: "B" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 759 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 698 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 766 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 742 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 731 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Conformer: "B" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} bond proxies already assigned to first conformer: 685 Conformer: "C" Number of residues, atoms: 89, 687 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain breaks: 1 bond proxies already assigned to first conformer: 685 Chain: "J" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1946 Classifications: {'DNA': 94} Link IDs: {'rna3p': 93} Chain: "I" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1908 Classifications: {'DNA': 94} Link IDs: {'rna3p': 93} Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 53 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} 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 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS H 82 " occ=0.31 ... (28 atoms not shown) pdb=" NE2CHIS H 82 " occ=0.37 residue: pdb=" N ATYR H 83 " occ=0.48 ... (22 atoms not shown) pdb=" OH BTYR H 83 " occ=0.52 Time building chain proxies: 2.42, per 1000 atoms: 0.25 Number of scatterers: 9678 At special positions: 0 Unit cell: (90.695, 114.07, 117.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 188 15.00 O 2169 8.00 N 1808 7.00 C 5499 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: 0.83 Conformation dependent library (CDL) restraints added in 353.2 milliseconds 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1390 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.4% alpha, 3.2% beta 88 base pairs and 168 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 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 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.502A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.692A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.545A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.470A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 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 removed outlier: 3.561A pdb=" N GLY D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.694A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.704A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 removed outlier: 4.113A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.661A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.549A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.551A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.826A pdb=" N SER H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.562A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU H 113 " --> pdb=" O HIS H 109 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.178A 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 96 through 98 removed outlier: 6.397A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.133A 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: 6.977A 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: 7.226A 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 78 387 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 224 hydrogen bonds 448 hydrogen bond angles 0 basepair planarities 88 basepair parallelities 168 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 1.11 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: 1903 1.33 - 1.45: 3047 1.45 - 1.57: 4876 1.57 - 1.69: 374 1.69 - 1.81: 26 Bond restraints: 10226 Sorted by residual: bond pdb=" C LEU H 101 " pdb=" N LEU H 102 " ideal model delta sigma weight residual 1.331 1.302 0.029 2.07e-02 2.33e+03 2.03e+00 bond pdb=" C LYS F 31 " pdb=" N PRO F 32 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.85e+00 bond pdb=" CB GLU H 93 " pdb=" CG GLU H 93 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" SD MET H 59 " pdb=" CE MET H 59 " ideal model delta sigma weight residual 1.791 1.764 0.027 2.50e-02 1.60e+03 1.16e+00 bond pdb=" C3' DT I 34 " pdb=" C2' DT I 34 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.05e+00 ... (remaining 10221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 13794 1.31 - 2.62: 725 2.62 - 3.93: 84 3.93 - 5.24: 8 5.24 - 6.55: 5 Bond angle restraints: 14616 Sorted by residual: angle pdb=" N VAL H 48 " pdb=" CA VAL H 48 " pdb=" C VAL H 48 " ideal model delta sigma weight residual 111.90 108.47 3.43 8.10e-01 1.52e+00 1.79e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.50 117.29 -5.79 1.74e+00 3.30e-01 1.11e+01 angle pdb=" CA GLY D 53 " pdb=" C GLY D 53 " pdb=" N ILE D 54 " ideal model delta sigma weight residual 114.55 117.81 -3.26 1.16e+00 7.43e-01 7.91e+00 angle pdb=" N GLY E 44 " pdb=" CA GLY E 44 " pdb=" C GLY E 44 " ideal model delta sigma weight residual 113.18 119.73 -6.55 2.37e+00 1.78e-01 7.64e+00 angle pdb=" C LEU H 80 " pdb=" N ALA H 81 " pdb=" CA ALA H 81 " ideal model delta sigma weight residual 120.34 123.91 -3.57 1.42e+00 4.96e-01 6.32e+00 ... (remaining 14611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3627 18.00 - 36.00: 988 36.00 - 53.99: 828 53.99 - 71.99: 223 71.99 - 89.99: 14 Dihedral angle restraints: 5680 sinusoidal: 3523 harmonic: 2157 Sorted by residual: dihedral pdb=" CA GLY G 67 " pdb=" C GLY G 67 " pdb=" N ASN G 68 " pdb=" CA ASN G 68 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CB GLU G 92 " pdb=" CG GLU G 92 " pdb=" CD GLU G 92 " pdb=" OE1 GLU G 92 " ideal model delta sinusoidal sigma weight residual 0.00 85.29 -85.29 1 3.00e+01 1.11e-03 9.79e+00 ... (remaining 5677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1266 0.042 - 0.084: 344 0.084 - 0.126: 57 0.126 - 0.168: 4 0.168 - 0.209: 1 Chirality restraints: 1672 Sorted by residual: chirality pdb=" CA TYR E 41 " pdb=" N TYR E 41 " pdb=" C TYR E 41 " pdb=" CB TYR E 41 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE D 89 " pdb=" N ILE D 89 " pdb=" C ILE D 89 " pdb=" CB ILE D 89 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CB VAL C 30 " pdb=" CA VAL C 30 " pdb=" CG1 VAL C 30 " pdb=" CG2 VAL C 30 " both_signs ideal model delta sigma weight residual False -2.63 -2.76 0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 1669 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 42 " -0.009 2.00e-02 2.50e+03 1.37e-02 3.78e+00 pdb=" CG TYR H 42 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR H 42 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR H 42 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR H 42 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 42 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR H 42 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 42 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 31 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO F 32 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO D 103 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.025 5.00e-02 4.00e+02 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 621 2.72 - 3.27: 8340 3.27 - 3.81: 18782 3.81 - 4.36: 23615 4.36 - 4.90: 34101 Nonbonded interactions: 85459 Sorted by model distance: nonbonded pdb=" NH2 ARG E 72 " pdb=" OP1 DC I -23 " model vdw 2.179 3.120 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.221 3.040 nonbonded pdb=" NH2 ARG G 32 " pdb=" OP2 DA I -44 " model vdw 2.279 3.120 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.294 3.040 nonbonded pdb=" OD1 ASP C 90 " pdb=" NH2 ARG L 367 " model vdw 2.308 3.120 ... (remaining 85454 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' and (resid 41 through 133 or (resid 134 through 135 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 41 through 114 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB )) or resid 116 through 135)) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 through 35 or (resid 36 and (name N or name CA or name C or name \ O or name CB )) or resid 37 through 113 or (resid 114 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'G' and (resid 17 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 73 or (resid 74 and (name N or nam \ e CA or name C or name O or name CB )) or resid 75 through 90 or (resid 91 and ( \ name N or name CA or name C or name O or name CB )) or resid 92 through 98 or (r \ esid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 th \ rough 111 or (resid 112 through 114 and (name N or name CA or name C or name O o \ r name CB )))) } ncs_group { reference = (chain 'D' and (resid 35 through 81 or resid 84 through 123)) selection = (chain 'H' and (resid 35 through 81 or resid 84 through 123)) } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 361 through 363 or (resid 364 and (name N or name CA or na \ me C or name O or name CB )) or resid 365 through 367)) } 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=0.31 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.004 0.035 10226 Z= 0.193 Angle : 0.658 6.552 14616 Z= 0.411 Chirality : 0.037 0.209 1672 Planarity : 0.005 0.047 1203 Dihedral : 28.228 89.989 4290 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.49 % Allowed : 28.07 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.30), residues: 727 helix: 0.63 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.90 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.030 0.002 TYR H 42 PHE 0.010 0.002 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00416 (10226) covalent geometry : angle 0.65761 (14616) hydrogen bonds : bond 0.13940 ( 611) hydrogen bonds : angle 5.34064 ( 1597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.294 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 130 average time/residue: 0.9427 time to fit residues: 127.8698 Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 366 SER Chi-restraints excluded: chain K residue 366 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN D 95 GLN F 25 ASN ** H 84 ASN ** 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 = 0.3927 r_free = 0.3927 target = 0.167338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132010 restraints weight = 33380.322| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.72 r_work: 0.3288 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10226 Z= 0.165 Angle : 0.565 6.714 14616 Z= 0.339 Chirality : 0.035 0.129 1672 Planarity : 0.005 0.044 1203 Dihedral : 29.609 89.816 2903 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.82 % Allowed : 26.58 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.30), residues: 727 helix: 1.41 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.86 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.019 0.001 TYR H 42 PHE 0.011 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00366 (10226) covalent geometry : angle 0.56493 (14616) hydrogen bonds : bond 0.03741 ( 611) hydrogen bonds : angle 3.19182 ( 1597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.279 Fit side-chains REVERT: B 92 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7150 (ttp80) REVERT: D 116 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7991 (tttm) REVERT: F 59 LYS cc_start: 0.8696 (ttpp) cc_final: 0.8231 (tttt) REVERT: F 74 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7820 (mt-10) outliers start: 17 outliers final: 9 residues processed: 128 average time/residue: 0.9717 time to fit residues: 129.6708 Evaluate side-chains 117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 366 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126857 restraints weight = 33018.998| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.71 r_work: 0.3221 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10226 Z= 0.279 Angle : 0.625 6.382 14616 Z= 0.369 Chirality : 0.040 0.157 1672 Planarity : 0.005 0.049 1203 Dihedral : 29.822 86.358 2898 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.15 % Allowed : 24.58 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.30), residues: 727 helix: 1.39 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -1.02 (0.41), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 79 TYR 0.012 0.002 TYR D 121 PHE 0.011 0.002 PHE G 25 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00646 (10226) covalent geometry : angle 0.62495 (14616) hydrogen bonds : bond 0.04933 ( 611) hydrogen bonds : angle 3.33741 ( 1597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.337 Fit side-chains REVERT: B 92 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7017 (ttp80) REVERT: C 35 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7754 (mtm110) REVERT: D 57 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7013 (mtpp) REVERT: D 116 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7956 (tttm) REVERT: E 63 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7793 (mmp80) REVERT: F 74 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7780 (mt-10) REVERT: G 35 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.6802 (mtt90) outliers start: 25 outliers final: 13 residues processed: 130 average time/residue: 0.9437 time to fit residues: 128.0493 Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 86 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129458 restraints weight = 34318.544| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.74 r_work: 0.3246 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10226 Z= 0.159 Angle : 0.571 5.890 14616 Z= 0.344 Chirality : 0.036 0.138 1672 Planarity : 0.005 0.058 1203 Dihedral : 29.853 86.955 2896 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.16 % Allowed : 25.25 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.31), residues: 727 helix: 1.72 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -1.00 (0.41), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 79 TYR 0.013 0.001 TYR D 40 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00350 (10226) covalent geometry : angle 0.57119 (14616) hydrogen bonds : bond 0.03887 ( 611) hydrogen bonds : angle 3.20153 ( 1597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.290 Fit side-chains REVERT: A 79 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7872 (tttt) REVERT: A 120 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7618 (mtt) REVERT: B 92 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.6941 (ttp80) REVERT: D 57 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7102 (mtpp) REVERT: D 116 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8020 (tttm) REVERT: F 59 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8298 (tttt) REVERT: F 74 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7623 (mt-10) REVERT: G 35 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7009 (mtt90) REVERT: H 71 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7211 (tm-30) outliers start: 19 outliers final: 9 residues processed: 124 average time/residue: 0.9053 time to fit residues: 117.3572 Evaluate side-chains 125 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.163371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128658 restraints weight = 25660.181| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.50 r_work: 0.3261 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10226 Z= 0.228 Angle : 0.586 5.952 14616 Z= 0.349 Chirality : 0.038 0.128 1672 Planarity : 0.005 0.046 1203 Dihedral : 29.784 87.684 2896 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.82 % Allowed : 25.58 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.31), residues: 727 helix: 1.66 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.98 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.012 0.002 TYR D 121 PHE 0.010 0.002 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00524 (10226) covalent geometry : angle 0.58631 (14616) hydrogen bonds : bond 0.04391 ( 611) hydrogen bonds : angle 3.20865 ( 1597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.286 Fit side-chains REVERT: A 79 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7852 (tttt) REVERT: A 120 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7852 (mtt) REVERT: B 92 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7071 (ttp80) REVERT: C 35 ARG cc_start: 0.8178 (mtm180) cc_final: 0.7775 (mtm110) REVERT: D 57 LYS cc_start: 0.8117 (mmtt) cc_final: 0.6993 (mtpp) REVERT: D 116 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7963 (tttm) REVERT: F 74 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7700 (mt-10) REVERT: G 35 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6929 (mtt90) outliers start: 23 outliers final: 12 residues processed: 129 average time/residue: 0.9673 time to fit residues: 130.1931 Evaluate side-chains 132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 86 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.163451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128972 restraints weight = 24967.289| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.48 r_work: 0.3268 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10226 Z= 0.226 Angle : 0.582 6.027 14616 Z= 0.347 Chirality : 0.038 0.148 1672 Planarity : 0.005 0.045 1203 Dihedral : 29.772 88.382 2896 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.49 % Allowed : 25.75 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.30), residues: 727 helix: 1.67 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.012 0.002 TYR G 57 PHE 0.010 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00520 (10226) covalent geometry : angle 0.58211 (14616) hydrogen bonds : bond 0.04245 ( 611) hydrogen bonds : angle 3.19952 ( 1597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.293 Fit side-chains REVERT: A 79 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7844 (tttt) REVERT: A 120 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7853 (mtt) REVERT: B 92 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.6963 (ttp80) REVERT: C 35 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7768 (mtm110) REVERT: D 46 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7018 (tptp) REVERT: D 57 LYS cc_start: 0.8091 (mmtt) cc_final: 0.6944 (mtpp) REVERT: D 116 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7935 (tttm) REVERT: F 74 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7665 (mt-10) REVERT: G 35 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6929 (mtt90) outliers start: 21 outliers final: 12 residues processed: 128 average time/residue: 0.9580 time to fit residues: 127.8965 Evaluate side-chains 132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 86 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128614 restraints weight = 29858.841| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.62 r_work: 0.3256 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10226 Z= 0.205 Angle : 0.575 5.873 14616 Z= 0.344 Chirality : 0.037 0.132 1672 Planarity : 0.005 0.045 1203 Dihedral : 29.774 88.456 2896 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.16 % Allowed : 26.58 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.31), residues: 727 helix: 1.69 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.93 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 TYR 0.022 0.002 TYR H 40 PHE 0.011 0.002 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00468 (10226) covalent geometry : angle 0.57549 (14616) hydrogen bonds : bond 0.04127 ( 611) hydrogen bonds : angle 3.20098 ( 1597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.296 Fit side-chains REVERT: A 79 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7841 (tttt) REVERT: A 120 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7862 (mtt) REVERT: B 92 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.6982 (ttp80) REVERT: C 35 ARG cc_start: 0.8173 (mtm180) cc_final: 0.7772 (mtm110) REVERT: D 46 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7011 (tptp) REVERT: D 57 LYS cc_start: 0.8115 (mmtt) cc_final: 0.6975 (mtpp) REVERT: D 116 LYS cc_start: 0.8469 (tptm) cc_final: 0.7943 (tttm) REVERT: F 74 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7677 (mt-10) REVERT: G 35 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.6943 (mtt90) outliers start: 19 outliers final: 13 residues processed: 128 average time/residue: 0.9502 time to fit residues: 126.9273 Evaluate side-chains 131 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 86 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.164348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129066 restraints weight = 32012.516| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.69 r_work: 0.3242 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10226 Z= 0.177 Angle : 0.566 5.726 14616 Z= 0.340 Chirality : 0.036 0.169 1672 Planarity : 0.005 0.049 1203 Dihedral : 29.775 88.520 2896 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.99 % Allowed : 26.08 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.31), residues: 727 helix: 1.75 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.88 (0.42), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 29 TYR 0.023 0.002 TYR H 40 PHE 0.011 0.002 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00395 (10226) covalent geometry : angle 0.56611 (14616) hydrogen bonds : bond 0.03968 ( 611) hydrogen bonds : angle 3.18185 ( 1597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.293 Fit side-chains REVERT: A 79 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7866 (tttt) REVERT: A 120 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7718 (mtt) REVERT: B 92 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6933 (ttp80) REVERT: C 35 ARG cc_start: 0.8153 (mtm180) cc_final: 0.7802 (mtm110) REVERT: D 46 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7145 (tptp) REVERT: D 57 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7071 (mtpp) REVERT: D 116 LYS cc_start: 0.8408 (tptm) cc_final: 0.8015 (tttm) REVERT: F 74 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7550 (mt-10) REVERT: G 35 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.6988 (mtt90) outliers start: 18 outliers final: 12 residues processed: 126 average time/residue: 0.9436 time to fit residues: 124.0126 Evaluate side-chains 130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 86 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.164026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129075 restraints weight = 32815.595| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.66 r_work: 0.3245 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10226 Z= 0.198 Angle : 0.565 5.879 14616 Z= 0.338 Chirality : 0.036 0.134 1672 Planarity : 0.005 0.045 1203 Dihedral : 29.728 88.945 2896 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.32 % Allowed : 25.42 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.31), residues: 727 helix: 1.74 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.86 (0.42), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 79 TYR 0.021 0.002 TYR H 40 PHE 0.011 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00451 (10226) covalent geometry : angle 0.56480 (14616) hydrogen bonds : bond 0.03935 ( 611) hydrogen bonds : angle 3.15564 ( 1597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.232 Fit side-chains REVERT: A 79 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7873 (tttt) REVERT: A 120 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7695 (mtt) REVERT: B 92 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6940 (ttp80) REVERT: C 35 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7809 (mtm110) REVERT: D 46 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7138 (tptp) REVERT: D 57 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7059 (mtpp) REVERT: D 116 LYS cc_start: 0.8398 (tptm) cc_final: 0.7998 (tttm) REVERT: F 74 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7557 (mt-10) REVERT: G 35 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7043 (mtt90) REVERT: G 75 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.6677 (tptt) outliers start: 20 outliers final: 14 residues processed: 128 average time/residue: 0.8454 time to fit residues: 112.9759 Evaluate side-chains 133 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 86 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 0.4980 chunk 77 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.164463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130220 restraints weight = 26418.314| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.48 r_work: 0.3271 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10226 Z= 0.170 Angle : 0.560 5.633 14616 Z= 0.337 Chirality : 0.035 0.149 1672 Planarity : 0.005 0.063 1203 Dihedral : 29.727 88.974 2896 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.32 % Allowed : 25.91 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.31), residues: 727 helix: 1.80 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.84 (0.42), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 TYR 0.023 0.002 TYR H 40 PHE 0.011 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00376 (10226) covalent geometry : angle 0.56004 (14616) hydrogen bonds : bond 0.03813 ( 611) hydrogen bonds : angle 3.13956 ( 1597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.247 Fit side-chains REVERT: A 79 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7886 (tttt) REVERT: A 120 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7779 (mtt) REVERT: B 92 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7029 (ttp80) REVERT: C 35 ARG cc_start: 0.8227 (mtm180) cc_final: 0.7869 (mtm110) REVERT: D 46 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7145 (tptp) REVERT: D 57 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7066 (mtpp) REVERT: D 116 LYS cc_start: 0.8489 (tptm) cc_final: 0.8037 (tttm) REVERT: F 74 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7733 (mt-10) REVERT: G 35 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7068 (mtt90) outliers start: 20 outliers final: 14 residues processed: 126 average time/residue: 0.8460 time to fit residues: 111.3387 Evaluate side-chains 132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 86 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.164948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130060 restraints weight = 32073.458| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.65 r_work: 0.3259 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10226 Z= 0.155 Angle : 0.554 5.572 14616 Z= 0.333 Chirality : 0.035 0.155 1672 Planarity : 0.005 0.080 1203 Dihedral : 29.724 88.992 2896 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.49 % Allowed : 26.74 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.31), residues: 727 helix: 1.84 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.82 (0.43), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 29 TYR 0.024 0.002 TYR H 40 PHE 0.012 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00338 (10226) covalent geometry : angle 0.55399 (14616) hydrogen bonds : bond 0.03729 ( 611) hydrogen bonds : angle 3.12333 ( 1597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4190.70 seconds wall clock time: 71 minutes 55.47 seconds (4315.47 seconds total)