Starting phenix.real_space_refine on Wed Feb 4 11:01:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rnh_54092/02_2026/9rnh_54092.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rnh_54092/02_2026/9rnh_54092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rnh_54092/02_2026/9rnh_54092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rnh_54092/02_2026/9rnh_54092.map" model { file = "/net/cci-nas-00/data/ceres_data/9rnh_54092/02_2026/9rnh_54092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rnh_54092/02_2026/9rnh_54092.cif" } resolution = 3.1 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= 0.002 sd= 0.064 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6735 2.51 5 N 1577 2.21 5 O 1718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10102 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1129 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1134 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1127 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1132 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 2 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: "E" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1379 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 178} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1332 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1370 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 177} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1364 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'OLC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'OLC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.45, per 1000 atoms: 0.24 Number of scatterers: 10102 At special positions: 0 Unit cell: (113.085, 111.793, 94.9914, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1718 8.00 N 1577 7.00 C 6735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS D 611 " distance=2.04 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS C 611 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.04 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 355.8 milliseconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 69.0% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 544 through 568 removed outlier: 3.758A pdb=" N VAL A 552 " --> pdb=" O TRP A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.545A pdb=" N TRP A 600 " --> pdb=" O PHE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 652 removed outlier: 3.640A pdb=" N THR A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 907 removed outlier: 3.642A pdb=" N TYR A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 907 " --> pdb=" O TYR A 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 569 removed outlier: 4.553A pdb=" N SER B 569 " --> pdb=" O VAL B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 607 Processing helix chain 'B' and resid 617 through 651 Processing helix chain 'B' and resid 815 through 843 removed outlier: 3.655A pdb=" N TYR B 819 " --> pdb=" O ALA B 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 568 removed outlier: 3.613A pdb=" N SER C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 608 removed outlier: 3.688A pdb=" N LEU C 599 " --> pdb=" O ILE C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 648 removed outlier: 3.816A pdb=" N VAL C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA C 643 " --> pdb=" O THR C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 841 Processing helix chain 'D' and resid 544 through 569 removed outlier: 3.515A pdb=" N VAL D 560 " --> pdb=" O ILE D 556 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER D 569 " --> pdb=" O VAL D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 607 removed outlier: 3.535A pdb=" N SER D 598 " --> pdb=" O GLY D 594 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU D 599 " --> pdb=" O ILE D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 646 Processing helix chain 'D' and resid 814 through 908 removed outlier: 4.104A pdb=" N PHE D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 835 " --> pdb=" O VAL D 831 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 30 Processing helix chain 'E' and resid 94 through 105 removed outlier: 3.911A pdb=" N LEU E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 125 removed outlier: 3.819A pdb=" N VAL E 112 " --> pdb=" O PRO E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.912A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 211 removed outlier: 3.538A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 30 Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 105 through 128 removed outlier: 3.858A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 161 removed outlier: 4.133A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER F 137 " --> pdb=" O ASN F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 212 Processing helix chain 'G' and resid 8 through 30 Processing helix chain 'G' and resid 94 through 105 Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.509A pdb=" N ILE G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 160 removed outlier: 3.611A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 212 Processing helix chain 'H' and resid 8 through 30 Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 105 through 123 Processing helix chain 'H' and resid 132 through 160 removed outlier: 3.809A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 212 removed outlier: 3.525A pdb=" N ILE H 188 " --> pdb=" O ALA H 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 34 through 38 removed outlier: 3.549A pdb=" N GLY E 38 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS E 67 " --> pdb=" O HIS E 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.617A pdb=" N CYS F 67 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 77 through 79 removed outlier: 3.651A pdb=" N CYS G 67 " --> pdb=" O HIS G 60 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER G 175 " --> pdb=" O TYR G 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.930A pdb=" N CYS H 67 " --> pdb=" O HIS H 60 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 2229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1820 1.33 - 1.46: 3223 1.46 - 1.59: 5196 1.59 - 1.71: 0 1.71 - 1.84: 112 Bond restraints: 10351 Sorted by residual: bond pdb=" N CYS D 837 " pdb=" CA CYS D 837 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.40e+00 bond pdb=" N CYS A 837 " pdb=" CA CYS A 837 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.51e+00 bond pdb=" C1 PLM D1001 " pdb=" O2 PLM D1001 " ideal model delta sigma weight residual 1.249 1.207 0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" C1 PLM A1001 " pdb=" O2 PLM A1001 " ideal model delta sigma weight residual 1.249 1.207 0.042 2.00e-02 2.50e+03 4.34e+00 bond pdb=" C1 PLM A1001 " pdb=" C2 PLM A1001 " ideal model delta sigma weight residual 1.542 1.502 0.040 2.00e-02 2.50e+03 4.00e+00 ... (remaining 10346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 13533 1.35 - 2.71: 370 2.71 - 4.06: 67 4.06 - 5.41: 20 5.41 - 6.76: 3 Bond angle restraints: 13993 Sorted by residual: angle pdb=" CA CYS D 837 " pdb=" C CYS D 837 " pdb=" O CYS D 837 " ideal model delta sigma weight residual 120.90 117.92 2.98 1.07e+00 8.73e-01 7.73e+00 angle pdb=" CA CYS A 837 " pdb=" C CYS A 837 " pdb=" O CYS A 837 " ideal model delta sigma weight residual 120.82 117.94 2.88 1.05e+00 9.07e-01 7.52e+00 angle pdb=" C PHE F 73 " pdb=" N LYS F 74 " pdb=" CA LYS F 74 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.16e+00 angle pdb=" CA CYS C 611 " pdb=" CB CYS C 611 " pdb=" SG CYS C 611 " ideal model delta sigma weight residual 114.40 120.35 -5.95 2.30e+00 1.89e-01 6.70e+00 angle pdb=" C GLN B 609 " pdb=" N GLY B 610 " pdb=" CA GLY B 610 " ideal model delta sigma weight residual 121.41 126.42 -5.01 1.96e+00 2.60e-01 6.53e+00 ... (remaining 13988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 5602 23.43 - 46.85: 230 46.85 - 70.28: 56 70.28 - 93.70: 4 93.70 - 117.13: 6 Dihedral angle restraints: 5898 sinusoidal: 2210 harmonic: 3688 Sorted by residual: dihedral pdb=" CB CYS B 611 " pdb=" SG CYS B 611 " pdb=" SG CYS C 611 " pdb=" CB CYS C 611 " ideal model delta sinusoidal sigma weight residual -86.00 -0.32 -85.68 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual -86.00 -36.26 -49.74 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS E 67 " pdb=" SG CYS E 67 " pdb=" SG CYS E 77 " pdb=" CB CYS E 77 " ideal model delta sinusoidal sigma weight residual -86.00 -125.92 39.92 1 1.00e+01 1.00e-02 2.24e+01 ... (remaining 5895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1160 0.039 - 0.078: 362 0.078 - 0.117: 53 0.117 - 0.156: 11 0.156 - 0.195: 3 Chirality restraints: 1589 Sorted by residual: chirality pdb=" CB VAL D 648 " pdb=" CA VAL D 648 " pdb=" CG1 VAL D 648 " pdb=" CG2 VAL D 648 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CB THR F 66 " pdb=" CA THR F 66 " pdb=" OG1 THR F 66 " pdb=" CG2 THR F 66 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CB THR E 66 " pdb=" CA THR E 66 " pdb=" OG1 THR E 66 " pdb=" CG2 THR E 66 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 1586 not shown) Planarity restraints: 1687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLC D1002 " -0.035 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C11 OLC D1002 " 0.033 2.00e-02 2.50e+03 pdb=" C8 OLC D1002 " 0.032 2.00e-02 2.50e+03 pdb=" C9 OLC D1002 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 588 " -0.052 5.00e-02 4.00e+02 7.87e-02 9.92e+00 pdb=" N PRO B 589 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 131 " -0.246 9.50e-02 1.11e+02 1.11e-01 9.75e+00 pdb=" NE ARG G 131 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG G 131 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG G 131 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG G 131 " -0.000 2.00e-02 2.50e+03 ... (remaining 1684 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1712 2.76 - 3.30: 10033 3.30 - 3.83: 17094 3.83 - 4.37: 19192 4.37 - 4.90: 33960 Nonbonded interactions: 81991 Sorted by model distance: nonbonded pdb=" O ILE F 122 " pdb=" OG SER F 125 " model vdw 2.226 3.040 nonbonded pdb=" O ILE H 140 " pdb=" OG SER H 144 " model vdw 2.374 3.040 nonbonded pdb=" O ASN F 133 " pdb=" ND2 ASN F 133 " model vdw 2.388 3.120 nonbonded pdb=" O ILE F 140 " pdb=" OG SER F 144 " model vdw 2.390 3.040 nonbonded pdb=" O ASN F 160 " pdb=" ND2 ASN F 160 " model vdw 2.410 3.120 ... (remaining 81986 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 533 through 648 or (resid 649 through 650 and (name N or n \ ame CA or name C or name O or name CB )) or resid 651 or resid 653 through 908)) \ selection = (chain 'B' and (resid 533 through 574 or (resid 588 and (name N or name CA or na \ me C or name O or name CB )) or resid 589 through 648 or (resid 649 through 650 \ and (name N or name CA or name C or name O or name CB )) or resid 651 or resid 8 \ 07 through 843)) selection = (chain 'C' and (resid 533 through 573 or (resid 574 through 588 and (name N or n \ ame CA or name C or name O or name CB )) or resid 589 through 651 or resid 807 t \ hrough 843)) selection = (chain 'D' and (resid 533 through 573 or (resid 574 through 588 and (name N or n \ ame CA or name C or name O or name CB )) or resid 589 through 648 or (resid 649 \ through 650 and (name N or name CA or name C or name O or name CB )) or resid 65 \ 1 or resid 807 through 908)) } ncs_group { reference = (chain 'E' and (resid 7 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 41 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 71 or (resid 72 and (n \ ame N or name CA or name C or name O or name CB )) or resid 73 or (resid 74 and \ (name N or name CA or name C or name O or name CB )) or resid 75 through 81 or ( \ resid 82 and (name N or name CA or name C or name O or name CB )) or resid 83 th \ rough 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) o \ r resid 98 through 161 or resid 173 through 212)) selection = (chain 'F' and (resid 7 through 40 or (resid 41 through 56 and (name N or name C \ A or name C or name O or name CB )) or resid 57 through 71 or (resid 72 and (nam \ e N or name CA or name C or name O or name CB )) or resid 73 through 161 or resi \ d 173 through 212)) selection = (chain 'G' and (resid 7 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 41 or resid 56 through 71 or (resid \ 72 and (name N or name CA or name C or name O or name CB )) or resid 73 through \ 81 or (resid 82 and (name N or name CA or name C or name O or name CB )) or res \ id 83 through 96 or (resid 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 161 or resid 173 through 212)) selection = (chain 'H' and (resid 7 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or (resid 56 and (name N or name CA or nam \ e C or name O or name CB )) or resid 57 through 81 or (resid 82 and (name N or n \ ame CA or name C or name O or name CB )) or resid 83 through 96 or (resid 97 and \ (name N or name CA or name C or name O or name CB )) or resid 98 through 161 or \ resid 173 through 212)) } 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=1.00 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: 9.920 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.320 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 0.042 10363 Z= 0.163 Angle : 0.550 6.763 14013 Z= 0.295 Chirality : 0.038 0.195 1589 Planarity : 0.011 0.111 1687 Dihedral : 13.911 117.130 3502 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -1.90 (0.22), residues: 1238 helix: -0.24 (0.16), residues: 888 sheet: -4.64 (0.78), residues: 20 loop : -3.78 (0.27), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.006 ARG G 131 TYR 0.012 0.001 TYR A 555 PHE 0.019 0.001 PHE F 182 TRP 0.013 0.001 TRP D 600 HIS 0.006 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00354 (10351) covalent geometry : angle 0.54572 (13993) SS BOND : bond 0.00474 ( 10) SS BOND : angle 1.84548 ( 20) hydrogen bonds : bond 0.21432 ( 752) hydrogen bonds : angle 6.77790 ( 2229) Misc. bond : bond 0.00350 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.359 Fit side-chains REVERT: E 22 SER cc_start: 0.8253 (m) cc_final: 0.8045 (m) REVERT: F 66 THR cc_start: 0.8752 (t) cc_final: 0.8365 (p) REVERT: H 24 MET cc_start: 0.8132 (tpt) cc_final: 0.7793 (tpt) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.0937 time to fit residues: 30.8572 Evaluate side-chains 165 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN C 609 GLN D 609 GLN F 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111647 restraints weight = 12894.810| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.03 r_work: 0.3121 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10363 Z= 0.140 Angle : 0.519 5.958 14013 Z= 0.283 Chirality : 0.038 0.185 1589 Planarity : 0.004 0.037 1687 Dihedral : 7.927 79.372 1481 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.84 % Allowed : 6.99 % Favored : 91.17 % 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: 1.26 (0.24), residues: 1238 helix: 2.16 (0.17), residues: 892 sheet: -3.58 (1.03), residues: 21 loop : -2.85 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 204 TYR 0.019 0.001 TYR E 174 PHE 0.016 0.002 PHE H 201 TRP 0.007 0.001 TRP H 64 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00301 (10351) covalent geometry : angle 0.51238 (13993) SS BOND : bond 0.00835 ( 10) SS BOND : angle 2.28761 ( 20) hydrogen bonds : bond 0.05171 ( 752) hydrogen bonds : angle 3.73463 ( 2229) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.230 Fit side-chains REVERT: D 572 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8508 (mp0) REVERT: E 79 GLN cc_start: 0.7627 (mt0) cc_final: 0.6938 (tm-30) REVERT: E 174 TYR cc_start: 0.8517 (p90) cc_final: 0.8132 (p90) REVERT: H 24 MET cc_start: 0.8689 (tpt) cc_final: 0.8361 (tpt) REVERT: H 58 MET cc_start: 0.8173 (mpp) cc_final: 0.7298 (mmm) REVERT: H 199 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7626 (m-70) outliers start: 19 outliers final: 10 residues processed: 175 average time/residue: 0.0940 time to fit residues: 22.9473 Evaluate side-chains 157 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain D residue 905 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 62 optimal weight: 9.9990 chunk 120 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 79 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 609 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.144128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112852 restraints weight = 12864.331| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.04 r_work: 0.3155 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10363 Z= 0.114 Angle : 0.488 12.438 14013 Z= 0.261 Chirality : 0.036 0.179 1589 Planarity : 0.003 0.036 1687 Dihedral : 7.265 61.616 1481 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % Rotamer: Outliers : 2.62 % Allowed : 8.74 % Favored : 88.64 % 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: 2.42 (0.25), residues: 1238 helix: 3.02 (0.17), residues: 891 sheet: -3.32 (0.88), residues: 20 loop : -2.43 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 209 TYR 0.013 0.001 TYR A 903 PHE 0.013 0.001 PHE H 201 TRP 0.005 0.001 TRP B 573 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00250 (10351) covalent geometry : angle 0.47036 (13993) SS BOND : bond 0.00463 ( 10) SS BOND : angle 3.46376 ( 20) hydrogen bonds : bond 0.04312 ( 752) hydrogen bonds : angle 3.37971 ( 2229) Misc. bond : bond 0.00008 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.330 Fit side-chains REVERT: D 572 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8595 (mp0) REVERT: D 611 CYS cc_start: 0.4162 (OUTLIER) cc_final: 0.3056 (p) REVERT: E 79 GLN cc_start: 0.7599 (mt0) cc_final: 0.6995 (tm-30) REVERT: E 174 TYR cc_start: 0.8473 (p90) cc_final: 0.8170 (p90) REVERT: G 37 ARG cc_start: 0.7251 (ttm110) cc_final: 0.7006 (ttm110) REVERT: H 24 MET cc_start: 0.8720 (tpt) cc_final: 0.8407 (tpt) REVERT: H 58 MET cc_start: 0.8221 (mpp) cc_final: 0.7564 (mmm) outliers start: 27 outliers final: 16 residues processed: 177 average time/residue: 0.0894 time to fit residues: 22.0252 Evaluate side-chains 160 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain D residue 611 CYS Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 52 optimal weight: 0.3980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 609 GLN H 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111835 restraints weight = 12944.927| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.03 r_work: 0.3112 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10363 Z= 0.114 Angle : 0.505 18.785 14013 Z= 0.267 Chirality : 0.037 0.352 1589 Planarity : 0.003 0.034 1687 Dihedral : 6.823 55.111 1481 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 2.23 % Allowed : 10.97 % Favored : 86.80 % 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: 2.88 (0.25), residues: 1238 helix: 3.35 (0.17), residues: 899 sheet: -3.57 (0.65), residues: 40 loop : -2.18 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 616 TYR 0.009 0.001 TYR C 545 PHE 0.013 0.001 PHE H 201 TRP 0.010 0.001 TRP B 573 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00233 (10351) covalent geometry : angle 0.49401 (13993) SS BOND : bond 0.01536 ( 10) SS BOND : angle 2.80332 ( 20) hydrogen bonds : bond 0.03853 ( 752) hydrogen bonds : angle 3.15048 ( 2229) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.245 Fit side-chains REVERT: D 572 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8561 (mp0) REVERT: E 79 GLN cc_start: 0.7750 (mt0) cc_final: 0.6991 (tm-30) REVERT: E 129 LYS cc_start: 0.8371 (mmtt) cc_final: 0.8020 (mmtp) REVERT: E 174 TYR cc_start: 0.8521 (p90) cc_final: 0.8189 (p90) REVERT: G 11 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7686 (mm) REVERT: G 37 ARG cc_start: 0.7255 (ttm110) cc_final: 0.7048 (ttm110) REVERT: H 10 MET cc_start: 0.8375 (tpt) cc_final: 0.8134 (tpt) REVERT: H 58 MET cc_start: 0.8289 (mpp) cc_final: 0.7565 (mmm) outliers start: 23 outliers final: 16 residues processed: 174 average time/residue: 0.0912 time to fit residues: 22.2739 Evaluate side-chains 170 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 840 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain D residue 905 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 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 = 0.3675 r_free = 0.3675 target = 0.144643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113231 restraints weight = 12721.403| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.04 r_work: 0.3111 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10363 Z= 0.114 Angle : 0.469 12.911 14013 Z= 0.247 Chirality : 0.036 0.201 1589 Planarity : 0.003 0.033 1687 Dihedral : 6.613 53.839 1481 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 1.94 % Allowed : 11.84 % Favored : 86.21 % 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: 3.07 (0.25), residues: 1238 helix: 3.40 (0.17), residues: 900 sheet: -2.22 (0.85), residues: 30 loop : -2.06 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 616 TYR 0.012 0.001 TYR A 903 PHE 0.013 0.001 PHE H 201 TRP 0.008 0.001 TRP B 573 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00254 (10351) covalent geometry : angle 0.45325 (13993) SS BOND : bond 0.00673 ( 10) SS BOND : angle 3.20269 ( 20) hydrogen bonds : bond 0.03832 ( 752) hydrogen bonds : angle 3.10118 ( 2229) Misc. bond : bond 0.00021 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.288 Fit side-chains REVERT: A 616 ARG cc_start: 0.8718 (mtm180) cc_final: 0.8350 (mtp-110) REVERT: E 79 GLN cc_start: 0.7799 (mt0) cc_final: 0.7112 (tm-30) REVERT: E 129 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8060 (mmtp) REVERT: E 174 TYR cc_start: 0.8582 (p90) cc_final: 0.8226 (p90) REVERT: G 11 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7679 (mm) REVERT: G 37 ARG cc_start: 0.7286 (ttm110) cc_final: 0.7069 (ttm110) REVERT: H 24 MET cc_start: 0.8671 (tpt) cc_final: 0.8287 (tpt) REVERT: H 58 MET cc_start: 0.8227 (mpp) cc_final: 0.7423 (mmt) REVERT: H 98 LEU cc_start: 0.7031 (tt) cc_final: 0.6598 (mm) outliers start: 20 outliers final: 15 residues processed: 172 average time/residue: 0.0879 time to fit residues: 21.1823 Evaluate side-chains 169 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 905 SER Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 0.2980 chunk 25 optimal weight: 0.2980 chunk 107 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 80 optimal weight: 0.0170 chunk 16 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114470 restraints weight = 12858.865| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.00 r_work: 0.3184 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10363 Z= 0.094 Angle : 0.417 7.763 14013 Z= 0.223 Chirality : 0.035 0.170 1589 Planarity : 0.003 0.032 1687 Dihedral : 6.288 56.027 1481 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 2.23 % Allowed : 12.43 % Favored : 85.34 % 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: 3.35 (0.25), residues: 1238 helix: 3.59 (0.16), residues: 901 sheet: -1.85 (0.71), residues: 39 loop : -1.93 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 616 TYR 0.013 0.001 TYR A 903 PHE 0.010 0.001 PHE H 127 TRP 0.006 0.001 TRP H 178 HIS 0.003 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00191 (10351) covalent geometry : angle 0.40941 (13993) SS BOND : bond 0.00852 ( 10) SS BOND : angle 2.17647 ( 20) hydrogen bonds : bond 0.03524 ( 752) hydrogen bonds : angle 2.98654 ( 2229) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.364 Fit side-chains REVERT: A 616 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8314 (mtp-110) REVERT: E 79 GLN cc_start: 0.7732 (mt0) cc_final: 0.7094 (tm-30) REVERT: E 129 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8070 (mmtp) REVERT: E 174 TYR cc_start: 0.8559 (p90) cc_final: 0.8182 (p90) REVERT: G 11 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7639 (mm) REVERT: G 76 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7282 (tt) REVERT: H 37 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7867 (ttm110) REVERT: H 58 MET cc_start: 0.8144 (mpp) cc_final: 0.7381 (mmt) REVERT: H 98 LEU cc_start: 0.6988 (tt) cc_final: 0.6650 (mm) outliers start: 23 outliers final: 16 residues processed: 176 average time/residue: 0.0930 time to fit residues: 23.0016 Evaluate side-chains 170 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 905 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 813 ASN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.140998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109637 restraints weight = 12794.242| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.12 r_work: 0.3032 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10363 Z= 0.140 Angle : 0.461 7.353 14013 Z= 0.246 Chirality : 0.036 0.171 1589 Planarity : 0.003 0.030 1687 Dihedral : 6.498 56.199 1481 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.25 % Rotamer: Outliers : 2.14 % Allowed : 12.91 % Favored : 84.95 % 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: 3.16 (0.25), residues: 1238 helix: 3.42 (0.16), residues: 902 sheet: -2.07 (0.78), residues: 35 loop : -1.87 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 102 TYR 0.011 0.001 TYR A 903 PHE 0.017 0.001 PHE H 201 TRP 0.009 0.001 TRP F 64 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00321 (10351) covalent geometry : angle 0.45454 (13993) SS BOND : bond 0.00668 ( 10) SS BOND : angle 2.14023 ( 20) hydrogen bonds : bond 0.03973 ( 752) hydrogen bonds : angle 3.16284 ( 2229) Misc. bond : bond 0.00032 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.299 Fit side-chains REVERT: A 616 ARG cc_start: 0.8752 (mtm180) cc_final: 0.8315 (mtp-110) REVERT: E 78 LYS cc_start: 0.7637 (ttpp) cc_final: 0.7419 (ptmm) REVERT: E 79 GLN cc_start: 0.7764 (mt0) cc_final: 0.6958 (tm-30) REVERT: E 129 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8157 (mtpt) REVERT: E 174 TYR cc_start: 0.8564 (p90) cc_final: 0.8193 (p90) REVERT: G 11 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7579 (mm) REVERT: G 174 TYR cc_start: 0.8891 (p90) cc_final: 0.8683 (p90) REVERT: H 58 MET cc_start: 0.8101 (mpp) cc_final: 0.7391 (mmt) outliers start: 22 outliers final: 16 residues processed: 170 average time/residue: 0.1038 time to fit residues: 24.3237 Evaluate side-chains 171 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 905 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 14 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 641 ASN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108779 restraints weight = 12840.430| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.01 r_work: 0.3042 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10363 Z= 0.130 Angle : 0.455 8.272 14013 Z= 0.240 Chirality : 0.037 0.175 1589 Planarity : 0.003 0.031 1687 Dihedral : 6.620 57.020 1481 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 2.62 % Allowed : 12.72 % Favored : 84.66 % 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: 3.14 (0.25), residues: 1238 helix: 3.39 (0.16), residues: 902 sheet: -3.31 (0.83), residues: 31 loop : -1.67 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 616 TYR 0.015 0.001 TYR A 903 PHE 0.012 0.001 PHE H 201 TRP 0.013 0.001 TRP D 573 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00298 (10351) covalent geometry : angle 0.44969 (13993) SS BOND : bond 0.00591 ( 10) SS BOND : angle 1.89245 ( 20) hydrogen bonds : bond 0.03866 ( 752) hydrogen bonds : angle 3.15940 ( 2229) Misc. bond : bond 0.00032 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 616 ARG cc_start: 0.8717 (mtm180) cc_final: 0.8316 (mtp-110) REVERT: D 572 GLU cc_start: 0.8835 (mp0) cc_final: 0.8635 (mp0) REVERT: E 79 GLN cc_start: 0.7732 (mt0) cc_final: 0.7075 (tm-30) REVERT: G 11 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7621 (mm) REVERT: G 58 MET cc_start: 0.8639 (tpt) cc_final: 0.8372 (tpt) REVERT: G 76 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7267 (tt) REVERT: H 58 MET cc_start: 0.8118 (mpp) cc_final: 0.7428 (mmt) REVERT: H 78 LYS cc_start: 0.7010 (ptmt) cc_final: 0.6280 (pttp) outliers start: 27 outliers final: 22 residues processed: 174 average time/residue: 0.0919 time to fit residues: 22.1188 Evaluate side-chains 177 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 905 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 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 = 0.3601 r_free = 0.3601 target = 0.138652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108256 restraints weight = 12873.918| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.00 r_work: 0.3034 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10363 Z= 0.133 Angle : 0.458 6.873 14013 Z= 0.242 Chirality : 0.036 0.169 1589 Planarity : 0.003 0.030 1687 Dihedral : 6.634 57.885 1481 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.26 % Favored : 97.66 % Rotamer: Outliers : 2.62 % Allowed : 12.62 % Favored : 84.76 % 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: 3.16 (0.25), residues: 1238 helix: 3.36 (0.16), residues: 902 sheet: -2.23 (0.81), residues: 40 loop : -1.63 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 616 TYR 0.022 0.001 TYR H 174 PHE 0.015 0.001 PHE H 201 TRP 0.013 0.001 TRP D 573 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00306 (10351) covalent geometry : angle 0.45291 (13993) SS BOND : bond 0.00433 ( 10) SS BOND : angle 1.80919 ( 20) hydrogen bonds : bond 0.03907 ( 752) hydrogen bonds : angle 3.18263 ( 2229) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 616 ARG cc_start: 0.8716 (mtm180) cc_final: 0.8322 (mtp-110) REVERT: G 11 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7569 (mm) REVERT: G 76 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7280 (tt) REVERT: H 58 MET cc_start: 0.8087 (mpp) cc_final: 0.7497 (mmm) REVERT: H 78 LYS cc_start: 0.6972 (ptmt) cc_final: 0.6113 (pttp) outliers start: 27 outliers final: 21 residues processed: 176 average time/residue: 0.0808 time to fit residues: 19.8894 Evaluate side-chains 176 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 905 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108811 restraints weight = 12646.809| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.98 r_work: 0.3041 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10363 Z= 0.122 Angle : 0.459 7.931 14013 Z= 0.242 Chirality : 0.036 0.167 1589 Planarity : 0.003 0.053 1687 Dihedral : 6.511 55.949 1481 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 2.23 % Allowed : 12.91 % Favored : 84.85 % 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: 3.15 (0.25), residues: 1238 helix: 3.41 (0.16), residues: 902 sheet: -2.95 (0.74), residues: 40 loop : -1.70 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 209 TYR 0.024 0.001 TYR H 174 PHE 0.011 0.001 PHE A 568 TRP 0.013 0.001 TRP D 573 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00275 (10351) covalent geometry : angle 0.45209 (13993) SS BOND : bond 0.00431 ( 10) SS BOND : angle 2.09457 ( 20) hydrogen bonds : bond 0.03821 ( 752) hydrogen bonds : angle 3.17989 ( 2229) Misc. bond : bond 0.00029 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 616 ARG cc_start: 0.8710 (mtm180) cc_final: 0.8319 (mtp-110) REVERT: F 117 MET cc_start: 0.7871 (mtp) cc_final: 0.7488 (mtp) REVERT: G 11 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7594 (mm) REVERT: G 76 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7260 (tt) REVERT: H 58 MET cc_start: 0.8057 (mpp) cc_final: 0.7399 (mmt) REVERT: H 78 LYS cc_start: 0.6456 (ptmt) cc_final: 0.5650 (mtmm) outliers start: 23 outliers final: 20 residues processed: 170 average time/residue: 0.0938 time to fit residues: 22.3142 Evaluate side-chains 173 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 905 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain H residue 199 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 46 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 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 = 0.3590 r_free = 0.3590 target = 0.137941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107541 restraints weight = 12890.913| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.98 r_work: 0.3032 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10363 Z= 0.122 Angle : 0.453 7.931 14013 Z= 0.240 Chirality : 0.036 0.153 1589 Planarity : 0.003 0.044 1687 Dihedral : 6.374 55.537 1481 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 2.14 % Allowed : 13.20 % Favored : 84.66 % 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: 3.16 (0.25), residues: 1238 helix: 3.41 (0.16), residues: 902 sheet: -3.11 (0.68), residues: 45 loop : -1.60 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 209 TYR 0.024 0.001 TYR H 174 PHE 0.013 0.001 PHE H 201 TRP 0.014 0.001 TRP D 573 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00277 (10351) covalent geometry : angle 0.44671 (13993) SS BOND : bond 0.00462 ( 10) SS BOND : angle 2.08867 ( 20) hydrogen bonds : bond 0.03809 ( 752) hydrogen bonds : angle 3.17528 ( 2229) Misc. bond : bond 0.00025 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2406.75 seconds wall clock time: 41 minutes 45.25 seconds (2505.25 seconds total)