Starting phenix.real_space_refine on Wed Sep 17 18:45:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fps_29369/09_2025/8fps_29369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fps_29369/09_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_29369/09_2025/8fps_29369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fps_29369/09_2025/8fps_29369.map" model { file = "/net/cci-nas-00/data/ceres_data/8fps_29369/09_2025/8fps_29369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fps_29369/09_2025/8fps_29369.cif" } resolution = 2.38 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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.60, per 1000 atoms: 0.34 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: 0.79 Conformation dependent library (CDL) restraints added in 622.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.31 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: 1.78 Time building geometry restraints manager: 1.10 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 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 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 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 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: 3.140 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.030 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG G 209 TYR 0.021 0.001 TYR A 523 PHE 0.010 0.001 PHE G 107 TRP 0.007 0.001 TRP E 64 HIS 0.012 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00179 (10712) covalent geometry : angle 0.37055 (14506) SS BOND : bond 0.00084 ( 8) SS BOND : angle 0.21353 ( 16) hydrogen bonds : bond 0.13870 ( 855) hydrogen bonds : angle 3.96125 ( 2468) *********************** 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 : 0.381 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: 0.5253 time to fit residues: 88.2393 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 : 0.260 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.177950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139530 restraints weight = 22387.369| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 4.32 r_work: 0.2950 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0868 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= 0.165 Angle : 0.478 4.596 14522 Z= 0.270 Chirality : 0.037 0.123 1638 Planarity : 0.003 0.035 1766 Dihedral : 4.804 52.243 1447 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.55 % Allowed : 18.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.95 (0.23), residues: 1308 helix: 3.72 (0.16), residues: 928 sheet: 0.01 (0.68), residues: 60 loop : -0.46 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 209 TYR 0.016 0.002 TYR C 523 PHE 0.015 0.002 PHE G 107 TRP 0.009 0.001 TRP C 578 HIS 0.010 0.002 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00350 (10712) covalent geometry : angle 0.47758 (14506) SS BOND : bond 0.00220 ( 8) SS BOND : angle 0.43049 ( 16) hydrogen bonds : bond 0.06108 ( 855) hydrogen bonds : angle 3.46360 ( 2468) *********************** 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 175 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.429 Fit side-chains REVERT: G 58 MET cc_start: 0.6449 (OUTLIER) cc_final: 0.6210 (tpt) REVERT: H 174 TYR cc_start: 0.7692 (p90) cc_final: 0.7400 (p90) outliers start: 16 outliers final: 5 residues processed: 166 average time/residue: 0.5644 time to fit residues: 101.2058 Evaluate side-chains 154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.177900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128774 restraints weight = 28147.412| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.32 r_work: 0.2988 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10720 Z= 0.151 Angle : 0.455 4.565 14522 Z= 0.258 Chirality : 0.036 0.119 1638 Planarity : 0.003 0.036 1766 Dihedral : 4.041 41.447 1437 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.37 % Allowed : 18.74 % Favored : 79.89 % 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 aren not related in a simple way. whole: 3.82 (0.23), residues: 1308 helix: 3.65 (0.16), residues: 928 sheet: 0.61 (0.78), residues: 40 loop : -0.69 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 209 TYR 0.018 0.002 TYR C 523 PHE 0.014 0.002 PHE G 107 TRP 0.009 0.001 TRP C 578 HIS 0.009 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00316 (10712) covalent geometry : angle 0.45549 (14506) SS BOND : bond 0.00187 ( 8) SS BOND : angle 0.35841 ( 16) hydrogen bonds : bond 0.05734 ( 855) hydrogen bonds : angle 3.39510 ( 2468) *********************** 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 175 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.414 Fit side-chains REVERT: E 58 MET cc_start: 0.6629 (tpt) cc_final: 0.6212 (tpt) REVERT: G 58 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.6265 (tpt) outliers start: 15 outliers final: 7 residues processed: 167 average time/residue: 0.5625 time to fit residues: 101.2479 Evaluate side-chains 159 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 209 ARG Chi-restraints excluded: chain G residue 58 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 0.0670 chunk 37 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.180138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131549 restraints weight = 37219.838| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.47 r_work: 0.3015 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10720 Z= 0.107 Angle : 0.392 4.619 14522 Z= 0.222 Chirality : 0.034 0.109 1638 Planarity : 0.003 0.035 1766 Dihedral : 3.529 25.482 1435 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.92 % Allowed : 17.92 % Favored : 80.16 % 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 aren not related in a simple way. whole: 4.19 (0.23), residues: 1308 helix: 3.96 (0.16), residues: 930 sheet: 0.81 (0.80), residues: 40 loop : -0.69 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 209 TYR 0.018 0.001 TYR A 523 PHE 0.009 0.001 PHE G 107 TRP 0.008 0.001 TRP E 178 HIS 0.008 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00197 (10712) covalent geometry : angle 0.39181 (14506) SS BOND : bond 0.00078 ( 8) SS BOND : angle 0.21640 ( 16) hydrogen bonds : bond 0.04659 ( 855) hydrogen bonds : angle 3.14947 ( 2468) *********************** 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 194 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.427 Fit side-chains REVERT: D 825 MET cc_start: 0.3433 (OUTLIER) cc_final: 0.2980 (tpp) REVERT: E 11 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7446 (tp) REVERT: E 58 MET cc_start: 0.6667 (tpt) cc_final: 0.6256 (tpt) REVERT: E 90 GLU cc_start: 0.1234 (OUTLIER) cc_final: -0.0201 (pm20) REVERT: E 97 PHE cc_start: 0.6304 (t80) cc_final: 0.5836 (t80) REVERT: E 127 PHE cc_start: 0.5597 (OUTLIER) cc_final: 0.5350 (t80) REVERT: G 58 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.6156 (tpt) REVERT: G 90 GLU cc_start: 0.1034 (OUTLIER) cc_final: -0.0075 (pm20) REVERT: G 97 PHE cc_start: 0.6330 (t80) cc_final: 0.5806 (t80) REVERT: G 208 LEU cc_start: 0.6716 (mp) cc_final: 0.6510 (mt) REVERT: F 127 PHE cc_start: 0.6191 (OUTLIER) cc_final: 0.5177 (m-10) outliers start: 21 outliers final: 4 residues processed: 180 average time/residue: 0.5488 time to fit residues: 106.5199 Evaluate side-chains 169 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 MET 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 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 24 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 43 optimal weight: 0.0000 chunk 98 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.180093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131274 restraints weight = 38333.333| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.48 r_work: 0.3031 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10720 Z= 0.108 Angle : 0.391 4.633 14522 Z= 0.221 Chirality : 0.034 0.108 1638 Planarity : 0.003 0.037 1766 Dihedral : 3.424 14.062 1434 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.46 % Allowed : 19.29 % Favored : 79.25 % 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 aren not related in a simple way. whole: 4.26 (0.23), residues: 1308 helix: 3.99 (0.16), residues: 934 sheet: 0.80 (0.80), residues: 40 loop : -0.65 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 209 TYR 0.018 0.001 TYR C 523 PHE 0.012 0.001 PHE A 546 TRP 0.008 0.001 TRP E 178 HIS 0.007 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00200 (10712) covalent geometry : angle 0.39082 (14506) SS BOND : bond 0.00081 ( 8) SS BOND : angle 0.23094 ( 16) hydrogen bonds : bond 0.04656 ( 855) hydrogen bonds : angle 3.11965 ( 2468) *********************** 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 175 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.391 Fit side-chains REVERT: B 514 VAL cc_start: 0.7362 (t) cc_final: 0.7036 (p) REVERT: D 825 MET cc_start: 0.3411 (OUTLIER) cc_final: 0.2948 (tpp) REVERT: E 11 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7451 (tp) REVERT: E 58 MET cc_start: 0.6605 (tpt) cc_final: 0.6146 (tpt) REVERT: E 90 GLU cc_start: 0.0845 (OUTLIER) cc_final: -0.0239 (pm20) REVERT: E 97 PHE cc_start: 0.6315 (t80) cc_final: 0.5857 (t80) REVERT: G 58 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.6183 (tpt) REVERT: G 97 PHE cc_start: 0.6242 (t80) cc_final: 0.5758 (t80) outliers start: 16 outliers final: 7 residues processed: 165 average time/residue: 0.5387 time to fit residues: 95.9024 Evaluate side-chains 168 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 58 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 0.0670 chunk 4 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.180009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131483 restraints weight = 36139.396| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.45 r_work: 0.3037 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- 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 = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10720 Z= 0.108 Angle : 0.394 4.889 14522 Z= 0.223 Chirality : 0.035 0.121 1638 Planarity : 0.003 0.037 1766 Dihedral : 3.437 15.977 1434 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.74 % Allowed : 19.01 % Favored : 79.25 % 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 aren not related in a simple way. whole: 4.29 (0.23), residues: 1308 helix: 4.00 (0.16), residues: 934 sheet: 0.80 (0.80), residues: 40 loop : -0.62 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 209 TYR 0.019 0.001 TYR C 523 PHE 0.015 0.001 PHE A 546 TRP 0.008 0.001 TRP E 178 HIS 0.007 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00201 (10712) covalent geometry : angle 0.39404 (14506) SS BOND : bond 0.00110 ( 8) SS BOND : angle 0.22529 ( 16) hydrogen bonds : bond 0.04652 ( 855) hydrogen bonds : angle 3.10905 ( 2468) *********************** 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 177 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.414 Fit side-chains REVERT: D 825 MET cc_start: 0.3421 (OUTLIER) cc_final: 0.2949 (tpp) REVERT: E 11 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7492 (tp) REVERT: E 58 MET cc_start: 0.6617 (tpt) cc_final: 0.6126 (tpt) REVERT: E 90 GLU cc_start: 0.0947 (OUTLIER) cc_final: -0.0206 (pm20) REVERT: E 97 PHE cc_start: 0.6334 (t80) cc_final: 0.5852 (t80) REVERT: E 127 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.5402 (t80) REVERT: G 58 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.6229 (tpt) REVERT: G 97 PHE cc_start: 0.6290 (t80) cc_final: 0.5814 (t80) outliers start: 19 outliers final: 5 residues processed: 166 average time/residue: 0.5620 time to fit residues: 100.7987 Evaluate side-chains 162 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 MET 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 G residue 58 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 128 optimal weight: 3.9990 chunk 101 optimal weight: 0.0020 chunk 25 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 85 optimal weight: 0.0570 chunk 73 optimal weight: 0.7980 overall best weight: 0.3886 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.182769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132686 restraints weight = 33552.039| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.64 r_work: 0.3064 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1186 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= 0.093 Angle : 0.376 6.208 14522 Z= 0.210 Chirality : 0.034 0.123 1638 Planarity : 0.003 0.037 1766 Dihedral : 3.307 18.185 1434 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.19 % Allowed : 19.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.50 (0.23), residues: 1308 helix: 4.17 (0.15), residues: 936 sheet: None (None), residues: 0 loop : -0.41 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 209 TYR 0.010 0.001 TYR B 523 PHE 0.016 0.001 PHE C 546 TRP 0.009 0.001 TRP E 178 HIS 0.007 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00165 (10712) covalent geometry : angle 0.37581 (14506) SS BOND : bond 0.00125 ( 8) SS BOND : angle 0.22134 ( 16) hydrogen bonds : bond 0.04013 ( 855) hydrogen bonds : angle 2.96235 ( 2468) *********************** 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 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.398 Fit side-chains REVERT: E 11 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7483 (tp) REVERT: E 58 MET cc_start: 0.6576 (tpt) cc_final: 0.6167 (tpt) REVERT: E 90 GLU cc_start: 0.0799 (OUTLIER) cc_final: -0.0239 (pm20) REVERT: E 97 PHE cc_start: 0.6197 (t80) cc_final: 0.5708 (t80) REVERT: G 58 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.6179 (tpt) REVERT: G 97 PHE cc_start: 0.6142 (t80) cc_final: 0.5635 (t80) REVERT: H 127 PHE cc_start: 0.6084 (OUTLIER) cc_final: 0.5160 (m-10) outliers start: 13 outliers final: 4 residues processed: 162 average time/residue: 0.5361 time to fit residues: 93.9164 Evaluate side-chains 162 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain G residue 58 MET 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 127 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 47 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.180602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129826 restraints weight = 39966.042| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.80 r_work: 0.3013 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10720 Z= 0.105 Angle : 0.390 5.342 14522 Z= 0.220 Chirality : 0.034 0.108 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.367 17.461 1434 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.91 % Allowed : 19.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.41 (0.23), residues: 1308 helix: 4.07 (0.15), residues: 936 sheet: None (None), residues: 0 loop : -0.36 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 209 TYR 0.015 0.001 TYR A 523 PHE 0.010 0.001 PHE E 107 TRP 0.007 0.001 TRP E 178 HIS 0.006 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00195 (10712) covalent geometry : angle 0.39031 (14506) SS BOND : bond 0.00082 ( 8) SS BOND : angle 0.23959 ( 16) hydrogen bonds : bond 0.04531 ( 855) hydrogen bonds : angle 3.06050 ( 2468) *********************** 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 166 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.406 Fit side-chains REVERT: E 11 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7452 (tp) REVERT: E 58 MET cc_start: 0.6545 (tpt) cc_final: 0.6133 (tpt) REVERT: E 90 GLU cc_start: 0.0894 (OUTLIER) cc_final: -0.0227 (pm20) REVERT: E 97 PHE cc_start: 0.6193 (t80) cc_final: 0.5731 (t80) REVERT: G 58 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.6210 (tpt) REVERT: G 97 PHE cc_start: 0.6213 (t80) cc_final: 0.5732 (t80) outliers start: 10 outliers final: 6 residues processed: 160 average time/residue: 0.5625 time to fit residues: 97.2341 Evaluate side-chains 164 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 58 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.179578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128320 restraints weight = 35928.359| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.68 r_work: 0.3014 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10720 Z= 0.110 Angle : 0.400 5.598 14522 Z= 0.226 Chirality : 0.035 0.108 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.415 16.891 1434 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.01 % Allowed : 19.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.34 (0.23), residues: 1308 helix: 4.04 (0.15), residues: 934 sheet: 0.78 (0.80), residues: 40 loop : -0.58 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 209 TYR 0.013 0.001 TYR A 549 PHE 0.011 0.001 PHE G 107 TRP 0.007 0.001 TRP E 178 HIS 0.006 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00207 (10712) covalent geometry : angle 0.40061 (14506) SS BOND : bond 0.00111 ( 8) SS BOND : angle 0.23459 ( 16) hydrogen bonds : bond 0.04681 ( 855) hydrogen bonds : angle 3.10451 ( 2468) *********************** 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 164 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.441 Fit side-chains REVERT: E 11 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7466 (tp) REVERT: E 58 MET cc_start: 0.6611 (tpt) cc_final: 0.6189 (tpt) REVERT: E 90 GLU cc_start: 0.0881 (OUTLIER) cc_final: -0.0243 (pm20) REVERT: E 97 PHE cc_start: 0.6241 (t80) cc_final: 0.5786 (t80) REVERT: G 58 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.6221 (tpt) REVERT: G 97 PHE cc_start: 0.6255 (t80) cc_final: 0.5784 (t80) outliers start: 11 outliers final: 6 residues processed: 157 average time/residue: 0.5572 time to fit residues: 94.3962 Evaluate side-chains 161 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 58 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.177797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126355 restraints weight = 35852.657| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.67 r_work: 0.2995 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 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 = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10720 Z= 0.151 Angle : 0.460 6.020 14522 Z= 0.258 Chirality : 0.037 0.118 1638 Planarity : 0.003 0.036 1766 Dihedral : 3.646 16.715 1434 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.82 % Allowed : 19.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.01 (0.23), residues: 1308 helix: 3.77 (0.16), residues: 932 sheet: 0.66 (0.80), residues: 40 loop : -0.59 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 209 TYR 0.018 0.002 TYR C 549 PHE 0.015 0.002 PHE G 107 TRP 0.009 0.001 TRP C 578 HIS 0.006 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00322 (10712) covalent geometry : angle 0.45974 (14506) SS BOND : bond 0.00196 ( 8) SS BOND : angle 0.33218 ( 16) hydrogen bonds : bond 0.05582 ( 855) hydrogen bonds : angle 3.29794 ( 2468) ********************** 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 167 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.332 Fit side-chains REVERT: E 58 MET cc_start: 0.6566 (tpt) cc_final: 0.6138 (tpt) REVERT: E 90 GLU cc_start: 0.1038 (OUTLIER) cc_final: -0.0126 (pm20) REVERT: E 97 PHE cc_start: 0.6286 (t80) cc_final: 0.5827 (t80) REVERT: G 58 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.6128 (tpt) REVERT: G 97 PHE cc_start: 0.6273 (t80) cc_final: 0.5810 (t80) outliers start: 9 outliers final: 6 residues processed: 161 average time/residue: 0.5282 time to fit residues: 91.7154 Evaluate side-chains 165 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 58 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.179606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128182 restraints weight = 33056.215| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.67 r_work: 0.3014 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10720 Z= 0.111 Angle : 0.406 5.728 14522 Z= 0.229 Chirality : 0.035 0.109 1638 Planarity : 0.003 0.037 1766 Dihedral : 3.491 16.603 1434 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.73 % Allowed : 19.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.21 (0.23), residues: 1308 helix: 3.94 (0.16), residues: 934 sheet: 0.70 (0.80), residues: 40 loop : -0.59 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 209 TYR 0.012 0.001 TYR B 523 PHE 0.012 0.001 PHE G 107 TRP 0.006 0.001 TRP C 578 HIS 0.006 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00211 (10712) covalent geometry : angle 0.40569 (14506) SS BOND : bond 0.00110 ( 8) SS BOND : angle 0.23187 ( 16) hydrogen bonds : bond 0.04766 ( 855) hydrogen bonds : angle 3.14067 ( 2468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4385.57 seconds wall clock time: 75 minutes 14.65 seconds (4514.65 seconds total)