Starting phenix.real_space_refine on Mon Jun 9 10:38:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fps_29369/06_2025/8fps_29369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fps_29369/06_2025/8fps_29369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fps_29369/06_2025/8fps_29369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fps_29369/06_2025/8fps_29369.map" model { file = "/net/cci-nas-00/data/ceres_data/8fps_29369/06_2025/8fps_29369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fps_29369/06_2025/8fps_29369.cif" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 S 74 5.16 5 Cl 4 4.86 5 C 6884 2.51 5 N 1662 2.21 5 O 1978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1159 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1165 Chain: "B" Number of atoms: 1190 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1184 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 151, 1184 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1209 Chain: "C" Number of atoms: 1159 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1165 Chain: "D" Number of atoms: 1190 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1184 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 151, 1184 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1209 Chain: "E" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1435 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 183} 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: "G" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1435 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 183} 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: "F" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1439 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1439 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "G" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 589 " occ=0.50 residue: pdb=" N ASER A 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 615 " occ=0.50 residue: pdb=" N ACYS B 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 589 " occ=0.50 residue: pdb=" N ACYS C 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 589 " occ=0.50 residue: pdb=" N ASER C 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 615 " occ=0.50 residue: pdb=" N ACYS D 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 589 " occ=0.50 Time building chain proxies: 9.71, per 1000 atoms: 0.92 Number of scatterers: 10602 At special positions: 0 Unit cell: (112.203, 110.565, 86.814, 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) Cl 4 17.00 S 74 16.00 O 1978 8.00 N 1662 7.00 C 6884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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 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 F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 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=2.03 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: 2.77 Conformation dependent library (CDL) restraints added in 1.9 seconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 74.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 826 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 624 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 826 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 826 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 624 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 826 Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 70 through 74 removed outlier: 4.170A pdb=" N PHE E 73 " --> pdb=" O GLU E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 105 removed outlier: 3.611A pdb=" N TYR E 96 " --> pdb=" O ASP E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 Processing helix chain 'E' and resid 132 through 160 removed outlier: 3.699A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 211 Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 70 through 74 removed outlier: 4.159A pdb=" N PHE G 73 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 removed outlier: 3.570A pdb=" N TYR G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.842A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 160 removed outlier: 3.713A 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 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 105 through 129 removed outlier: 3.524A pdb=" N ILE F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.633A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 212 Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 92 through 105 Processing helix chain 'H' and resid 105 through 129 removed outlier: 3.508A pdb=" N ILE H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.651A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 212 Processing sheet with id=AA1, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'H' and resid 77 through 79 855 hydrogen bonds defined for protein. 2468 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: 3.11 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3146 1.34 - 1.46: 2871 1.46 - 1.58: 4583 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 10712 Sorted by residual: bond pdb=" N GLY B 588 " pdb=" CA GLY B 588 " ideal model delta sigma weight residual 1.447 1.454 -0.008 1.09e-02 8.42e+03 5.19e-01 bond pdb=" C VAL C 792 " pdb=" O VAL C 792 " ideal model delta sigma weight residual 1.231 1.241 -0.010 1.51e-02 4.39e+03 3.97e-01 bond pdb=" N GLY D 588 " pdb=" CA GLY D 588 " ideal model delta sigma weight residual 1.447 1.453 -0.007 1.09e-02 8.42e+03 3.96e-01 bond pdb=" C PHE D 607 " pdb=" O PHE D 607 " ideal model delta sigma weight residual 1.236 1.244 -0.007 1.15e-02 7.56e+03 3.80e-01 bond pdb=" C VAL A 792 " pdb=" O VAL A 792 " ideal model delta sigma weight residual 1.235 1.244 -0.008 1.45e-02 4.76e+03 3.42e-01 ... (remaining 10707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 14102 0.94 - 1.88: 334 1.88 - 2.82: 45 2.82 - 3.76: 15 3.76 - 4.70: 10 Bond angle restraints: 14506 Sorted by residual: angle pdb=" CA TYR C 523 " pdb=" CB TYR C 523 " pdb=" CG TYR C 523 " ideal model delta sigma weight residual 113.90 117.55 -3.65 1.80e+00 3.09e-01 4.12e+00 angle pdb=" CA TYR A 523 " pdb=" CB TYR A 523 " pdb=" CG TYR A 523 " ideal model delta sigma weight residual 113.90 117.19 -3.29 1.80e+00 3.09e-01 3.35e+00 angle pdb=" CA GLU A 550 " pdb=" CB GLU A 550 " pdb=" CG GLU A 550 " ideal model delta sigma weight residual 114.10 117.72 -3.62 2.00e+00 2.50e-01 3.27e+00 angle pdb=" CA GLU C 550 " pdb=" CB GLU C 550 " pdb=" CG GLU C 550 " ideal model delta sigma weight residual 114.10 117.42 -3.32 2.00e+00 2.50e-01 2.76e+00 angle pdb=" N PHE F 107 " pdb=" CA PHE F 107 " pdb=" C PHE F 107 " ideal model delta sigma weight residual 109.81 113.32 -3.51 2.21e+00 2.05e-01 2.52e+00 ... (remaining 14501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5356 17.93 - 35.86: 551 35.86 - 53.79: 144 53.79 - 71.72: 36 71.72 - 89.65: 9 Dihedral angle restraints: 6096 sinusoidal: 2246 harmonic: 3850 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual -86.00 -131.23 45.23 1 1.00e+01 1.00e-02 2.84e+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 -131.16 45.16 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB GLU E 90 " pdb=" CG GLU E 90 " pdb=" CD GLU E 90 " pdb=" OE1 GLU E 90 " ideal model delta sinusoidal sigma weight residual 0.00 89.65 -89.65 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 969 0.021 - 0.043: 327 0.043 - 0.064: 223 0.064 - 0.085: 90 0.085 - 0.107: 29 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CA PHE H 107 " pdb=" N PHE H 107 " pdb=" C PHE H 107 " pdb=" CB PHE H 107 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.84e-01 chirality pdb=" CA PRO A 520 " pdb=" N PRO A 520 " pdb=" C PRO A 520 " pdb=" CB PRO A 520 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.82e-01 chirality pdb=" CA PRO D 520 " pdb=" N PRO D 520 " pdb=" C PRO D 520 " pdb=" CB PRO D 520 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.81e-01 ... (remaining 1635 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 107 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO G 108 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO G 108 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 108 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 60 " -0.008 2.00e-02 2.50e+03 1.01e-02 1.53e+00 pdb=" CG HIS E 60 " 0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS E 60 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS E 60 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS E 60 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 60 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 107 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO E 108 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.017 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1396 2.75 - 3.29: 10427 3.29 - 3.83: 19341 3.83 - 4.36: 20648 4.36 - 4.90: 36556 Nonbonded interactions: 88368 Sorted by model distance: nonbonded pdb=" OG1 THR G 30 " pdb=" OG SER G 179 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR E 30 " pdb=" OG SER E 179 " model vdw 2.223 3.040 nonbonded pdb=" O SER E 105 " pdb=" OG SER E 105 " model vdw 2.232 3.040 nonbonded pdb=" O SER G 105 " pdb=" OG SER G 105 " model vdw 2.233 3.040 nonbonded pdb=" O HOH B 926 " pdb=" O HOH D 925 " model vdw 2.243 3.040 ... (remaining 88363 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 511 or (resid 512 and (name N or name CA or name C or name \ O or name CB )) or resid 513 through 588 or resid 590 through 614 or resid 616 \ through 625 or resid 784 through 826)) selection = (chain 'B' and (resid 511 through 552 or resid 566 through 588 or resid 590 thro \ ugh 614 or resid 616 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) selection = (chain 'C' and (resid 511 or (resid 512 and (name N or name CA or name C or name \ O or name CB )) or resid 513 through 588 or resid 590 through 614 or resid 616 \ through 625 or resid 784 through 826)) selection = (chain 'D' and (resid 511 through 552 or resid 566 through 588 or resid 590 thro \ ugh 614 or resid 616 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) } ncs_group { reference = (chain 'E' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 212 or resid 401)) selection = (chain 'F' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 212 or resid 401)) selection = (chain 'G' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 212 or resid 401)) selection = (chain 'H' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 212 or resid 401)) } 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=0.50 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: 3.240 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.650 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 : 0.002 0.022 10720 Z= 0.096 Angle : 0.370 4.700 14522 Z= 0.209 Chirality : 0.033 0.107 1638 Planarity : 0.002 0.031 1766 Dihedral : 16.267 89.649 3608 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.01 % Allowed : 19.20 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.23), residues: 1308 helix: 3.82 (0.15), residues: 930 sheet: 1.09 (0.82), residues: 40 loop : -0.50 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 64 HIS 0.012 0.001 HIS E 60 PHE 0.010 0.001 PHE G 107 TYR 0.021 0.001 TYR A 523 ARG 0.001 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.13870 ( 855) hydrogen bonds : angle 3.96125 ( 2468) SS BOND : bond 0.00084 ( 8) SS BOND : angle 0.21353 ( 16) covalent geometry : bond 0.00179 (10712) covalent geometry : angle 0.37055 (14506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 1.124 Fit side-chains REVERT: E 11 LEU cc_start: 0.7891 (tm) cc_final: 0.7600 (tp) REVERT: E 97 PHE cc_start: 0.6303 (t80) cc_final: 0.6001 (t80) REVERT: G 97 PHE cc_start: 0.6345 (t80) cc_final: 0.6012 (t80) outliers start: 10 outliers final: 9 residues processed: 155 average time/residue: 1.1172 time to fit residues: 188.4979 Evaluate side-chains 154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 120 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 HIS E 132 HIS G 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.178215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130462 restraints weight = 35278.569| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.49 r_work: 0.2993 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10720 Z= 0.156 Angle : 0.465 4.603 14522 Z= 0.263 Chirality : 0.037 0.121 1638 Planarity : 0.003 0.035 1766 Dihedral : 4.752 51.862 1447 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.37 % Allowed : 18.28 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.23), residues: 1308 helix: 3.78 (0.16), residues: 928 sheet: 0.03 (0.68), residues: 60 loop : -0.44 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 578 HIS 0.009 0.001 HIS E 60 PHE 0.014 0.002 PHE G 107 TYR 0.016 0.002 TYR C 523 ARG 0.004 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.05994 ( 855) hydrogen bonds : angle 3.43178 ( 2468) SS BOND : bond 0.00201 ( 8) SS BOND : angle 0.40150 ( 16) covalent geometry : bond 0.00329 (10712) covalent geometry : angle 0.46535 (14506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.257 Fit side-chains REVERT: G 58 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6285 (tpt) outliers start: 14 outliers final: 5 residues processed: 164 average time/residue: 1.1483 time to fit residues: 204.1261 Evaluate side-chains 153 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 124 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN E 132 HIS G 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.175342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120694 restraints weight = 27413.696| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.55 r_work: 0.2910 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10720 Z= 0.185 Angle : 0.503 4.540 14522 Z= 0.284 Chirality : 0.038 0.127 1638 Planarity : 0.004 0.037 1766 Dihedral : 4.273 44.159 1437 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.01 % Allowed : 17.73 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.23), residues: 1308 helix: 3.47 (0.16), residues: 928 sheet: 0.58 (0.78), residues: 40 loop : -0.75 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 578 HIS 0.007 0.001 HIS E 205 PHE 0.016 0.002 PHE G 107 TYR 0.019 0.002 TYR C 523 ARG 0.005 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.06314 ( 855) hydrogen bonds : angle 3.53421 ( 2468) SS BOND : bond 0.00255 ( 8) SS BOND : angle 0.43591 ( 16) covalent geometry : bond 0.00407 (10712) covalent geometry : angle 0.50275 (14506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 1.000 Fit side-chains REVERT: A 550 GLU cc_start: 0.6798 (pp20) cc_final: 0.6597 (pm20) REVERT: E 58 MET cc_start: 0.6679 (tpt) cc_final: 0.6250 (tpt) outliers start: 21 outliers final: 12 residues processed: 171 average time/residue: 1.5992 time to fit residues: 296.3197 Evaluate side-chains 167 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 4 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 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 = 0.4055 r_free = 0.4055 target = 0.181087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131426 restraints weight = 34764.365| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.66 r_work: 0.3036 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10720 Z= 0.100 Angle : 0.381 4.632 14522 Z= 0.216 Chirality : 0.034 0.108 1638 Planarity : 0.003 0.036 1766 Dihedral : 3.526 26.193 1437 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.83 % Allowed : 17.55 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (0.23), residues: 1308 helix: 3.95 (0.16), residues: 932 sheet: 0.79 (0.81), residues: 40 loop : -0.68 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 178 HIS 0.004 0.001 HIS E 205 PHE 0.008 0.001 PHE F 107 TYR 0.017 0.001 TYR A 523 ARG 0.002 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 855) hydrogen bonds : angle 3.11747 ( 2468) SS BOND : bond 0.00082 ( 8) SS BOND : angle 0.18033 ( 16) covalent geometry : bond 0.00176 (10712) covalent geometry : angle 0.38125 (14506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.093 Fit side-chains REVERT: C 514 VAL cc_start: 0.7023 (t) cc_final: 0.6720 (p) REVERT: E 11 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7454 (tp) REVERT: E 58 MET cc_start: 0.6653 (tpt) cc_final: 0.6228 (tpt) REVERT: E 90 GLU cc_start: 0.1046 (OUTLIER) cc_final: -0.0173 (pm20) REVERT: E 97 PHE cc_start: 0.6272 (t80) cc_final: 0.5787 (t80) REVERT: E 127 PHE cc_start: 0.5543 (OUTLIER) cc_final: 0.5323 (t80) REVERT: G 58 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.6134 (tpt) REVERT: G 90 GLU cc_start: 0.1060 (OUTLIER) cc_final: -0.0058 (pm20) REVERT: G 97 PHE cc_start: 0.6269 (t80) cc_final: 0.5731 (t80) REVERT: G 208 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6525 (mt) REVERT: F 127 PHE cc_start: 0.6165 (OUTLIER) cc_final: 0.5167 (m-10) outliers start: 20 outliers final: 4 residues processed: 183 average time/residue: 1.1033 time to fit residues: 219.0731 Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 88 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 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 = 0.4019 r_free = 0.4019 target = 0.177737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126263 restraints weight = 32206.153| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.67 r_work: 0.2978 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10720 Z= 0.146 Angle : 0.446 4.578 14522 Z= 0.252 Chirality : 0.036 0.117 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.670 15.296 1434 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.55 % Allowed : 19.01 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.23), residues: 1308 helix: 3.72 (0.16), residues: 932 sheet: 0.66 (0.82), residues: 40 loop : -0.67 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 578 HIS 0.005 0.001 HIS E 205 PHE 0.015 0.002 PHE G 107 TYR 0.019 0.002 TYR A 523 ARG 0.003 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.05591 ( 855) hydrogen bonds : angle 3.33364 ( 2468) SS BOND : bond 0.00210 ( 8) SS BOND : angle 0.33470 ( 16) covalent geometry : bond 0.00305 (10712) covalent geometry : angle 0.44624 (14506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.296 Fit side-chains REVERT: A 550 GLU cc_start: 0.6720 (pp20) cc_final: 0.6490 (pm20) REVERT: E 58 MET cc_start: 0.6670 (tpt) cc_final: 0.6192 (tpt) REVERT: E 90 GLU cc_start: 0.1071 (OUTLIER) cc_final: -0.0160 (pm20) REVERT: E 97 PHE cc_start: 0.6286 (t80) cc_final: 0.5796 (t80) REVERT: G 58 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.6157 (tpt) REVERT: G 97 PHE cc_start: 0.6297 (t80) cc_final: 0.5788 (t80) REVERT: G 208 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6633 (mt) outliers start: 17 outliers final: 8 residues processed: 171 average time/residue: 1.2763 time to fit residues: 236.8603 Evaluate side-chains 165 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 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 = 0.4034 r_free = 0.4034 target = 0.179170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130558 restraints weight = 35755.772| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.55 r_work: 0.2998 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10720 Z= 0.114 Angle : 0.406 5.607 14522 Z= 0.230 Chirality : 0.035 0.123 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.551 17.039 1434 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.55 % Allowed : 18.92 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.23), residues: 1308 helix: 3.87 (0.16), residues: 934 sheet: 0.73 (0.82), residues: 40 loop : -0.61 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.004 0.001 HIS E 205 PHE 0.012 0.001 PHE E 107 TYR 0.020 0.001 TYR A 523 ARG 0.002 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 855) hydrogen bonds : angle 3.18727 ( 2468) SS BOND : bond 0.00091 ( 8) SS BOND : angle 0.23835 ( 16) covalent geometry : bond 0.00218 (10712) covalent geometry : angle 0.40654 (14506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 1.475 Fit side-chains REVERT: B 514 VAL cc_start: 0.7387 (t) cc_final: 0.7048 (p) REVERT: E 11 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7446 (tp) REVERT: E 58 MET cc_start: 0.6673 (tpt) cc_final: 0.6331 (tpt) REVERT: E 90 GLU cc_start: 0.0945 (OUTLIER) cc_final: -0.0289 (pm20) REVERT: E 97 PHE cc_start: 0.6287 (t80) cc_final: 0.5781 (t80) REVERT: G 58 MET cc_start: 0.6402 (OUTLIER) cc_final: 0.6168 (tpt) REVERT: G 97 PHE cc_start: 0.6318 (t80) cc_final: 0.5805 (t80) REVERT: G 208 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6615 (mt) REVERT: H 127 PHE cc_start: 0.6068 (OUTLIER) cc_final: 0.5108 (m-10) outliers start: 17 outliers final: 8 residues processed: 171 average time/residue: 1.6628 time to fit residues: 307.7937 Evaluate side-chains 173 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 127 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 111 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 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 = 0.4024 r_free = 0.4024 target = 0.178156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127291 restraints weight = 33617.064| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.62 r_work: 0.2983 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10720 Z= 0.132 Angle : 0.432 5.383 14522 Z= 0.244 Chirality : 0.036 0.123 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.640 16.328 1434 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.55 % Allowed : 19.10 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.00 (0.23), residues: 1308 helix: 3.77 (0.16), residues: 932 sheet: 0.66 (0.82), residues: 40 loop : -0.62 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 578 HIS 0.005 0.001 HIS E 205 PHE 0.014 0.001 PHE G 107 TYR 0.021 0.002 TYR A 523 ARG 0.003 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.05298 ( 855) hydrogen bonds : angle 3.27573 ( 2468) SS BOND : bond 0.00146 ( 8) SS BOND : angle 0.28105 ( 16) covalent geometry : bond 0.00267 (10712) covalent geometry : angle 0.43235 (14506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.195 Fit side-chains REVERT: B 514 VAL cc_start: 0.7475 (t) cc_final: 0.7133 (p) REVERT: E 11 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7511 (tp) REVERT: E 58 MET cc_start: 0.6725 (tpt) cc_final: 0.6324 (tpt) REVERT: E 90 GLU cc_start: 0.0961 (OUTLIER) cc_final: -0.0279 (pm20) REVERT: E 97 PHE cc_start: 0.6308 (t80) cc_final: 0.5821 (t80) REVERT: G 58 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.6184 (tpt) REVERT: G 97 PHE cc_start: 0.6293 (t80) cc_final: 0.5792 (t80) outliers start: 17 outliers final: 7 residues processed: 167 average time/residue: 1.7278 time to fit residues: 315.1071 Evaluate side-chains 167 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 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 = 0.4034 r_free = 0.4034 target = 0.179132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.128002 restraints weight = 29560.511| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.65 r_work: 0.3010 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10720 Z= 0.115 Angle : 0.410 5.970 14522 Z= 0.231 Chirality : 0.035 0.122 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.542 15.500 1434 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.28 % Allowed : 19.38 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.14 (0.23), residues: 1308 helix: 3.87 (0.16), residues: 934 sheet: 0.70 (0.82), residues: 40 loop : -0.60 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 178 HIS 0.004 0.001 HIS E 205 PHE 0.014 0.001 PHE A 546 TYR 0.020 0.001 TYR A 523 ARG 0.002 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.04854 ( 855) hydrogen bonds : angle 3.17831 ( 2468) SS BOND : bond 0.00121 ( 8) SS BOND : angle 0.25066 ( 16) covalent geometry : bond 0.00222 (10712) covalent geometry : angle 0.41017 (14506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.257 Fit side-chains REVERT: C 550 GLU cc_start: 0.6551 (pm20) cc_final: 0.6286 (pp20) REVERT: E 11 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7461 (tp) REVERT: E 58 MET cc_start: 0.6627 (tpt) cc_final: 0.6267 (tpt) REVERT: E 90 GLU cc_start: 0.0918 (OUTLIER) cc_final: -0.0331 (pm20) REVERT: E 97 PHE cc_start: 0.6290 (t80) cc_final: 0.5778 (t80) REVERT: E 127 PHE cc_start: 0.5662 (OUTLIER) cc_final: 0.5367 (t80) REVERT: G 58 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.6172 (tpt) REVERT: G 90 GLU cc_start: 0.0869 (OUTLIER) cc_final: -0.0415 (pm20) REVERT: G 97 PHE cc_start: 0.6368 (t80) cc_final: 0.5863 (t80) outliers start: 14 outliers final: 9 residues processed: 168 average time/residue: 1.2467 time to fit residues: 226.6956 Evaluate side-chains 169 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 96 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 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 = 0.4021 r_free = 0.4021 target = 0.177955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127330 restraints weight = 35560.186| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.64 r_work: 0.2982 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10720 Z= 0.137 Angle : 0.441 5.770 14522 Z= 0.249 Chirality : 0.036 0.119 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.658 15.525 1434 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.28 % Allowed : 19.29 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.23), residues: 1308 helix: 3.73 (0.16), residues: 932 sheet: 0.62 (0.83), residues: 40 loop : -0.60 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 578 HIS 0.005 0.001 HIS E 205 PHE 0.014 0.002 PHE G 107 TYR 0.023 0.002 TYR C 523 ARG 0.003 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.05392 ( 855) hydrogen bonds : angle 3.29595 ( 2468) SS BOND : bond 0.00156 ( 8) SS BOND : angle 0.29700 ( 16) covalent geometry : bond 0.00281 (10712) covalent geometry : angle 0.44158 (14506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.251 Fit side-chains REVERT: C 550 GLU cc_start: 0.6550 (pm20) cc_final: 0.6266 (pp20) REVERT: E 58 MET cc_start: 0.6640 (tpt) cc_final: 0.6333 (tpt) REVERT: E 90 GLU cc_start: 0.0954 (OUTLIER) cc_final: -0.0284 (pm20) REVERT: E 97 PHE cc_start: 0.6339 (t80) cc_final: 0.5842 (t80) REVERT: E 127 PHE cc_start: 0.5748 (OUTLIER) cc_final: 0.5392 (t80) REVERT: G 58 MET cc_start: 0.6440 (OUTLIER) cc_final: 0.6202 (tpt) REVERT: G 90 GLU cc_start: 0.0899 (OUTLIER) cc_final: -0.0354 (pm20) REVERT: G 97 PHE cc_start: 0.6314 (t80) cc_final: 0.5811 (t80) outliers start: 14 outliers final: 10 residues processed: 166 average time/residue: 1.1966 time to fit residues: 214.8207 Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 0.0770 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 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 = 0.4018 r_free = 0.4018 target = 0.177641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125891 restraints weight = 31495.941| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.57 r_work: 0.2985 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10720 Z= 0.145 Angle : 0.455 5.815 14522 Z= 0.256 Chirality : 0.037 0.121 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.709 15.803 1434 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.37 % Allowed : 19.20 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.23), residues: 1308 helix: 3.66 (0.16), residues: 932 sheet: 0.58 (0.83), residues: 40 loop : -0.59 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 578 HIS 0.006 0.001 HIS E 205 PHE 0.019 0.002 PHE C 546 TYR 0.022 0.002 TYR A 523 ARG 0.002 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.05523 ( 855) hydrogen bonds : angle 3.33265 ( 2468) SS BOND : bond 0.00176 ( 8) SS BOND : angle 0.31837 ( 16) covalent geometry : bond 0.00302 (10712) covalent geometry : angle 0.45494 (14506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 1.237 Fit side-chains REVERT: A 550 GLU cc_start: 0.6781 (pp20) cc_final: 0.6542 (pm20) REVERT: E 58 MET cc_start: 0.6577 (tpt) cc_final: 0.6271 (tpt) REVERT: E 90 GLU cc_start: 0.0978 (OUTLIER) cc_final: -0.0260 (pm20) REVERT: E 127 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.5368 (t80) REVERT: G 58 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.6170 (tpt) REVERT: G 90 GLU cc_start: 0.0866 (OUTLIER) cc_final: -0.0346 (pm20) outliers start: 15 outliers final: 10 residues processed: 165 average time/residue: 1.1221 time to fit residues: 200.7590 Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 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 = 0.4019 r_free = 0.4019 target = 0.177759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126467 restraints weight = 35069.935| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.60 r_work: 0.2981 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10720 Z= 0.142 Angle : 0.451 6.202 14522 Z= 0.254 Chirality : 0.036 0.133 1638 Planarity : 0.003 0.037 1766 Dihedral : 3.707 15.903 1434 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.28 % Allowed : 19.10 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.23), residues: 1308 helix: 3.66 (0.16), residues: 932 sheet: 0.57 (0.83), residues: 40 loop : -0.57 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 578 HIS 0.005 0.001 HIS E 205 PHE 0.018 0.002 PHE C 546 TYR 0.021 0.002 TYR A 523 ARG 0.002 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.05469 ( 855) hydrogen bonds : angle 3.32651 ( 2468) SS BOND : bond 0.00172 ( 8) SS BOND : angle 0.31735 ( 16) covalent geometry : bond 0.00295 (10712) covalent geometry : angle 0.45101 (14506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9924.73 seconds wall clock time: 175 minutes 31.40 seconds (10531.40 seconds total)