Starting phenix.real_space_refine on Fri Aug 22 18:09:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvh_41642/08_2025/8tvh_41642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvh_41642/08_2025/8tvh_41642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tvh_41642/08_2025/8tvh_41642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvh_41642/08_2025/8tvh_41642.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvh_41642/08_2025/8tvh_41642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvh_41642/08_2025/8tvh_41642.cif" } resolution = 3.6 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= 0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 4290 2.51 5 N 1173 2.21 5 O 1263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6744 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 740 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 740 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 870 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 870 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 740 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 870 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 624 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 624 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 624 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.80, per 1000 atoms: 0.27 Number of scatterers: 6744 At special positions: 0 Unit cell: (118.02, 116.053, 92.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 1263 8.00 N 1173 7.00 C 4290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.16 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.16 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.17 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 459 " " NAG B 601 " - " ASN B 459 " " NAG C 601 " - " ASN C 459 " Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 378.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 15 sheets defined 32.3% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'A' and resid 136 through 177 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 451 through 477 Processing helix chain 'B' and resid 136 through 177 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 451 through 477 Processing helix chain 'C' and resid 136 through 177 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 451 through 477 Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.560A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.560A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.568A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.523A pdb=" N VAL G 99 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR G 33 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.568A pdb=" N SER F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.523A pdb=" N VAL F 99 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR F 33 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.560A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.567A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.523A pdb=" N VAL I 99 " --> pdb=" O TYR I 33 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TYR I 33 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 11 through 12 420 hydrogen bonds defined for protein. 1071 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: 0.98 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2011 1.33 - 1.47: 1847 1.47 - 1.60: 2988 1.60 - 1.74: 0 1.74 - 1.87: 24 Bond restraints: 6870 Sorted by residual: bond pdb=" CA ALA G 92 " pdb=" CB ALA G 92 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.69e-02 3.50e+03 1.06e+01 bond pdb=" CA ALA I 92 " pdb=" CB ALA I 92 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.69e-02 3.50e+03 1.05e+01 bond pdb=" CA ALA F 92 " pdb=" CB ALA F 92 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.69e-02 3.50e+03 1.04e+01 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.66e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.56e+00 ... (remaining 6865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 7579 1.59 - 3.18: 1457 3.18 - 4.77: 241 4.77 - 6.36: 91 6.36 - 7.95: 7 Bond angle restraints: 9375 Sorted by residual: angle pdb=" C ASP I 52 " pdb=" N PRO I 53 " pdb=" CA PRO I 53 " ideal model delta sigma weight residual 119.56 127.51 -7.95 1.02e+00 9.61e-01 6.08e+01 angle pdb=" C ASP G 52 " pdb=" N PRO G 53 " pdb=" CA PRO G 53 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.02e+00 9.61e-01 6.03e+01 angle pdb=" C ASP F 52 " pdb=" N PRO F 53 " pdb=" CA PRO F 53 " ideal model delta sigma weight residual 119.56 127.43 -7.87 1.02e+00 9.61e-01 5.96e+01 angle pdb=" C VAL H 58 " pdb=" N PRO H 59 " pdb=" CA PRO H 59 " ideal model delta sigma weight residual 119.78 126.05 -6.27 1.03e+00 9.43e-01 3.71e+01 angle pdb=" C VAL E 58 " pdb=" N PRO E 59 " pdb=" CA PRO E 59 " ideal model delta sigma weight residual 119.78 126.04 -6.26 1.03e+00 9.43e-01 3.70e+01 ... (remaining 9370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3883 17.55 - 35.09: 128 35.09 - 52.64: 36 52.64 - 70.18: 24 70.18 - 87.73: 6 Dihedral angle restraints: 4077 sinusoidal: 1380 harmonic: 2697 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.08 40.92 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " pdb=" CB CYS I 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.10 40.90 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.10 40.90 1 1.00e+01 1.00e-02 2.34e+01 ... (remaining 4074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 737 0.075 - 0.150: 282 0.150 - 0.224: 46 0.224 - 0.299: 9 0.299 - 0.374: 6 Chirality restraints: 1080 Sorted by residual: chirality pdb=" C2 NAG A 601 " pdb=" C1 NAG A 601 " pdb=" C3 NAG A 601 " pdb=" N2 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.87 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C2 NAG C 601 " pdb=" C1 NAG C 601 " pdb=" C3 NAG C 601 " pdb=" N2 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.86 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C2 NAG B 601 " pdb=" C1 NAG B 601 " pdb=" C3 NAG B 601 " pdb=" N2 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.86 0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 1077 not shown) Planarity restraints: 1233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 90 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" C ASP F 90 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP F 90 " 0.014 2.00e-02 2.50e+03 pdb=" N THR F 91 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 90 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ASP I 90 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP I 90 " 0.014 2.00e-02 2.50e+03 pdb=" N THR I 91 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 90 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ASP G 90 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP G 90 " -0.014 2.00e-02 2.50e+03 pdb=" N THR G 91 " -0.013 2.00e-02 2.50e+03 ... (remaining 1230 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 3267 2.97 - 3.45: 6161 3.45 - 3.94: 10882 3.94 - 4.42: 11893 4.42 - 4.90: 20334 Nonbonded interactions: 52537 Sorted by model distance: nonbonded pdb=" NZ LYS E 39 " pdb=" O GLU E 81 " model vdw 2.491 3.120 nonbonded pdb=" NZ LYS D 39 " pdb=" O GLU D 81 " model vdw 2.491 3.120 nonbonded pdb=" NZ LYS H 39 " pdb=" O GLU H 81 " model vdw 2.492 3.120 nonbonded pdb=" N THR F 87 " pdb=" O THR F 87 " model vdw 2.553 2.496 nonbonded pdb=" N THR G 87 " pdb=" O THR G 87 " model vdw 2.553 2.496 ... (remaining 52532 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: 0.02 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 10.170 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: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.690 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.013 0.134 6879 Z= 0.710 Angle : 1.393 7.951 9396 Z= 0.934 Chirality : 0.081 0.374 1080 Planarity : 0.006 0.022 1230 Dihedral : 12.107 87.727 2331 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.30 % Favored : 97.38 % Rotamer: Outliers : 0.52 % Allowed : 2.95 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.54 (0.26), residues: 915 helix: 1.99 (0.24), residues: 228 sheet: 1.62 (0.31), residues: 273 loop : 0.10 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 61 TYR 0.026 0.003 TYR E 36 PHE 0.017 0.004 PHE I 27 TRP 0.028 0.007 TRP G 47 HIS 0.004 0.002 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.01240 ( 6870) covalent geometry : angle 1.37761 ( 9375) SS BOND : bond 0.09503 ( 6) SS BOND : angle 3.53938 ( 12) hydrogen bonds : bond 0.18961 ( 405) hydrogen bonds : angle 6.45512 ( 1071) link_NAG-ASN : bond 0.06725 ( 3) link_NAG-ASN : angle 5.62580 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.266 Fit side-chains REVERT: F 38 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8672 (tttm) outliers start: 3 outliers final: 0 residues processed: 99 average time/residue: 0.0995 time to fit residues: 12.6533 Evaluate side-chains 66 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN D 89 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN A 157 GLN B 157 GLN C 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.130700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.111347 restraints weight = 8521.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.111347 restraints weight = 8120.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.111347 restraints weight = 8120.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.111347 restraints weight = 8120.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.111347 restraints weight = 8120.329| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6879 Z= 0.200 Angle : 0.650 7.430 9396 Z= 0.335 Chirality : 0.045 0.206 1080 Planarity : 0.004 0.033 1230 Dihedral : 5.200 40.857 1051 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.52 % Allowed : 8.33 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.77 (0.28), residues: 915 helix: 4.56 (0.24), residues: 231 sheet: 1.46 (0.30), residues: 309 loop : 0.40 (0.35), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 96 TYR 0.011 0.002 TYR G 33 PHE 0.011 0.002 PHE E 98 TRP 0.012 0.002 TRP F 47 HIS 0.001 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 6870) covalent geometry : angle 0.64467 ( 9375) SS BOND : bond 0.01283 ( 6) SS BOND : angle 2.11282 ( 12) hydrogen bonds : bond 0.06497 ( 405) hydrogen bonds : angle 5.15509 ( 1071) link_NAG-ASN : bond 0.00029 ( 3) link_NAG-ASN : angle 1.36069 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.242 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.0718 time to fit residues: 9.6870 Evaluate side-chains 76 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 12 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 85 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.128157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109177 restraints weight = 8464.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109177 restraints weight = 8349.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109177 restraints weight = 8349.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109177 restraints weight = 8349.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109177 restraints weight = 8349.086| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6879 Z= 0.166 Angle : 0.571 7.358 9396 Z= 0.293 Chirality : 0.042 0.136 1080 Planarity : 0.004 0.032 1230 Dihedral : 4.643 30.590 1047 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.04 % Allowed : 12.50 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.79 (0.29), residues: 915 helix: 5.07 (0.26), residues: 228 sheet: 1.33 (0.29), residues: 327 loop : 0.18 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 96 TYR 0.012 0.002 TYR E 49 PHE 0.012 0.002 PHE F 58 TRP 0.012 0.001 TRP F 47 HIS 0.002 0.000 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6870) covalent geometry : angle 0.56302 ( 9375) SS BOND : bond 0.00793 ( 6) SS BOND : angle 2.48517 ( 12) hydrogen bonds : bond 0.05234 ( 405) hydrogen bonds : angle 4.56476 ( 1071) link_NAG-ASN : bond 0.00056 ( 3) link_NAG-ASN : angle 1.31654 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.267 Fit side-chains REVERT: G 6 GLN cc_start: 0.8899 (tt0) cc_final: 0.8698 (tt0) REVERT: G 102 THR cc_start: 0.9409 (p) cc_final: 0.9135 (p) REVERT: F 102 THR cc_start: 0.9354 (p) cc_final: 0.9149 (p) REVERT: I 102 THR cc_start: 0.9346 (p) cc_final: 0.9118 (p) outliers start: 6 outliers final: 5 residues processed: 103 average time/residue: 0.0758 time to fit residues: 10.9357 Evaluate side-chains 98 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain F residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.107933 restraints weight = 8495.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.107933 restraints weight = 8538.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.107933 restraints weight = 8538.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.107933 restraints weight = 8538.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.107933 restraints weight = 8538.447| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6879 Z= 0.203 Angle : 0.610 6.659 9396 Z= 0.312 Chirality : 0.043 0.139 1080 Planarity : 0.004 0.032 1230 Dihedral : 4.696 25.484 1047 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.30 % Allowed : 13.02 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.55 (0.29), residues: 915 helix: 4.84 (0.28), residues: 228 sheet: 1.34 (0.29), residues: 327 loop : -0.11 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 171 TYR 0.012 0.002 TYR D 32 PHE 0.011 0.002 PHE H 98 TRP 0.011 0.002 TRP F 47 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 6870) covalent geometry : angle 0.59912 ( 9375) SS BOND : bond 0.01152 ( 6) SS BOND : angle 2.97547 ( 12) hydrogen bonds : bond 0.05555 ( 405) hydrogen bonds : angle 4.49734 ( 1071) link_NAG-ASN : bond 0.00282 ( 3) link_NAG-ASN : angle 1.49658 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.317 Fit side-chains REVERT: D 91 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8839 (m-80) REVERT: G 116 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8512 (m) REVERT: F 105 TYR cc_start: 0.9119 (m-80) cc_final: 0.8888 (m-80) REVERT: A 454 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6158 (mm-40) outliers start: 19 outliers final: 10 residues processed: 115 average time/residue: 0.0787 time to fit residues: 12.4907 Evaluate side-chains 101 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain A residue 454 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.153444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.137044 restraints weight = 7861.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.137805 restraints weight = 7227.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138030 restraints weight = 6830.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138030 restraints weight = 6624.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138030 restraints weight = 6624.746| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6879 Z= 0.158 Angle : 0.555 7.041 9396 Z= 0.281 Chirality : 0.041 0.136 1080 Planarity : 0.004 0.036 1230 Dihedral : 4.454 22.939 1047 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.99 % Allowed : 13.19 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.69 (0.29), residues: 915 helix: 4.99 (0.29), residues: 231 sheet: 1.19 (0.29), residues: 348 loop : 0.07 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 171 TYR 0.009 0.001 TYR E 49 PHE 0.012 0.001 PHE F 58 TRP 0.009 0.001 TRP I 47 HIS 0.002 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6870) covalent geometry : angle 0.54586 ( 9375) SS BOND : bond 0.00915 ( 6) SS BOND : angle 2.51244 ( 12) hydrogen bonds : bond 0.04863 ( 405) hydrogen bonds : angle 4.28409 ( 1071) link_NAG-ASN : bond 0.00015 ( 3) link_NAG-ASN : angle 1.54495 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.285 Fit side-chains REVERT: D 91 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8786 (m-80) REVERT: G 114 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8609 (t) REVERT: G 116 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8415 (m) REVERT: A 454 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.5999 (mm-40) outliers start: 23 outliers final: 13 residues processed: 107 average time/residue: 0.0785 time to fit residues: 11.9525 Evaluate side-chains 106 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 479 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 32 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.123835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.108098 restraints weight = 8441.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.108098 restraints weight = 8417.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.108098 restraints weight = 8417.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.108098 restraints weight = 8417.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.108098 restraints weight = 8417.685| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6879 Z= 0.166 Angle : 0.557 6.762 9396 Z= 0.281 Chirality : 0.041 0.134 1080 Planarity : 0.004 0.037 1230 Dihedral : 4.350 21.384 1047 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.47 % Allowed : 13.72 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.67 (0.29), residues: 915 helix: 4.96 (0.28), residues: 231 sheet: 1.26 (0.29), residues: 348 loop : -0.02 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 171 TYR 0.009 0.001 TYR D 49 PHE 0.012 0.001 PHE F 58 TRP 0.009 0.001 TRP F 47 HIS 0.003 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6870) covalent geometry : angle 0.54771 ( 9375) SS BOND : bond 0.00895 ( 6) SS BOND : angle 2.61392 ( 12) hydrogen bonds : bond 0.04845 ( 405) hydrogen bonds : angle 4.20542 ( 1071) link_NAG-ASN : bond 0.00100 ( 3) link_NAG-ASN : angle 1.63472 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.250 Fit side-chains REVERT: D 91 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8807 (m-80) REVERT: G 116 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8450 (m) REVERT: A 454 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.5991 (mm-40) outliers start: 20 outliers final: 14 residues processed: 103 average time/residue: 0.0717 time to fit residues: 10.4946 Evaluate side-chains 104 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 0.0970 chunk 66 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 0.0470 chunk 14 optimal weight: 0.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.162050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.144662 restraints weight = 7700.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.145554 restraints weight = 6862.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.146507 restraints weight = 6325.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.147234 restraints weight = 5928.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.147249 restraints weight = 5651.468| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6879 Z= 0.117 Angle : 0.514 7.396 9396 Z= 0.256 Chirality : 0.040 0.130 1080 Planarity : 0.004 0.038 1230 Dihedral : 4.100 18.862 1047 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.30 % Allowed : 14.76 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.81 (0.30), residues: 915 helix: 5.28 (0.28), residues: 231 sheet: 1.20 (0.29), residues: 348 loop : 0.07 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 171 TYR 0.009 0.001 TYR E 49 PHE 0.012 0.001 PHE F 58 TRP 0.009 0.001 TRP I 47 HIS 0.002 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6870) covalent geometry : angle 0.50623 ( 9375) SS BOND : bond 0.00706 ( 6) SS BOND : angle 2.21578 ( 12) hydrogen bonds : bond 0.04072 ( 405) hydrogen bonds : angle 3.96853 ( 1071) link_NAG-ASN : bond 0.00087 ( 3) link_NAG-ASN : angle 1.57441 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.270 Fit side-chains REVERT: D 91 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8706 (m-80) REVERT: G 116 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8264 (m) REVERT: A 454 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.5896 (mm-40) outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 0.0713 time to fit residues: 10.3830 Evaluate side-chains 104 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.138783 restraints weight = 7795.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139206 restraints weight = 7137.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139208 restraints weight = 6801.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139208 restraints weight = 6799.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139208 restraints weight = 6799.450| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6879 Z= 0.184 Angle : 0.569 6.649 9396 Z= 0.287 Chirality : 0.042 0.136 1080 Planarity : 0.004 0.036 1230 Dihedral : 4.190 16.993 1047 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.99 % Allowed : 13.89 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.54 (0.29), residues: 915 helix: 4.94 (0.28), residues: 231 sheet: 1.14 (0.29), residues: 351 loop : -0.13 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 171 TYR 0.010 0.001 TYR D 49 PHE 0.010 0.001 PHE F 58 TRP 0.007 0.001 TRP F 47 HIS 0.003 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 6870) covalent geometry : angle 0.55840 ( 9375) SS BOND : bond 0.00904 ( 6) SS BOND : angle 2.81622 ( 12) hydrogen bonds : bond 0.04894 ( 405) hydrogen bonds : angle 4.13415 ( 1071) link_NAG-ASN : bond 0.00172 ( 3) link_NAG-ASN : angle 1.77159 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.287 Fit side-chains REVERT: D 91 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8882 (m-80) REVERT: G 116 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8411 (m) REVERT: A 454 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6038 (mm-40) outliers start: 23 outliers final: 16 residues processed: 102 average time/residue: 0.0711 time to fit residues: 10.2953 Evaluate side-chains 103 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 479 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 0.0000 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.135323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.115214 restraints weight = 8288.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.115824 restraints weight = 7722.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 14)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.115932 restraints weight = 7336.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.115937 restraints weight = 7210.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.115937 restraints weight = 7208.132| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6879 Z= 0.159 Angle : 0.554 7.319 9396 Z= 0.277 Chirality : 0.041 0.134 1080 Planarity : 0.004 0.038 1230 Dihedral : 4.081 14.886 1047 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.47 % Allowed : 14.58 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.53 (0.30), residues: 915 helix: 5.03 (0.28), residues: 231 sheet: 1.13 (0.29), residues: 351 loop : -0.20 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 171 TYR 0.009 0.001 TYR E 49 PHE 0.010 0.001 PHE F 58 TRP 0.008 0.001 TRP I 47 HIS 0.003 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6870) covalent geometry : angle 0.54386 ( 9375) SS BOND : bond 0.00772 ( 6) SS BOND : angle 2.49861 ( 12) hydrogen bonds : bond 0.04598 ( 405) hydrogen bonds : angle 4.04710 ( 1071) link_NAG-ASN : bond 0.00070 ( 3) link_NAG-ASN : angle 1.84822 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.238 Fit side-chains REVERT: D 91 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8781 (m-80) REVERT: G 116 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8253 (m) REVERT: A 454 GLN cc_start: 0.7038 (OUTLIER) cc_final: 0.6070 (mm-40) outliers start: 20 outliers final: 16 residues processed: 99 average time/residue: 0.0665 time to fit residues: 9.3050 Evaluate side-chains 102 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 0.0070 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.0170 chunk 42 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 5 optimal weight: 0.0170 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.127453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.112412 restraints weight = 8338.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.111245 restraints weight = 8469.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.111175 restraints weight = 8937.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.111241 restraints weight = 9051.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.111258 restraints weight = 8824.391| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6879 Z= 0.103 Angle : 0.510 7.623 9396 Z= 0.253 Chirality : 0.040 0.129 1080 Planarity : 0.004 0.038 1230 Dihedral : 3.892 16.335 1047 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.95 % Allowed : 15.80 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.79 (0.30), residues: 915 helix: 5.44 (0.29), residues: 231 sheet: 1.20 (0.29), residues: 348 loop : -0.09 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 171 TYR 0.008 0.001 TYR G 109 PHE 0.014 0.001 PHE F 58 TRP 0.009 0.001 TRP I 47 HIS 0.002 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 6870) covalent geometry : angle 0.50244 ( 9375) SS BOND : bond 0.00621 ( 6) SS BOND : angle 2.08430 ( 12) hydrogen bonds : bond 0.03590 ( 405) hydrogen bonds : angle 3.82226 ( 1071) link_NAG-ASN : bond 0.00085 ( 3) link_NAG-ASN : angle 1.68919 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.271 Fit side-chains REVERT: D 91 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: A 454 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.5760 (mm-40) outliers start: 17 outliers final: 12 residues processed: 107 average time/residue: 0.0737 time to fit residues: 11.0833 Evaluate side-chains 102 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain B residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 78 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.154867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.139104 restraints weight = 7667.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.139781 restraints weight = 7041.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.139781 restraints weight = 6624.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.139781 restraints weight = 6624.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.139781 restraints weight = 6624.243| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6879 Z= 0.178 Angle : 0.577 7.304 9396 Z= 0.289 Chirality : 0.042 0.135 1080 Planarity : 0.004 0.036 1230 Dihedral : 4.007 15.695 1047 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.12 % Allowed : 16.32 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.54 (0.30), residues: 915 helix: 5.04 (0.28), residues: 231 sheet: 1.16 (0.29), residues: 351 loop : -0.24 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 171 TYR 0.010 0.002 TYR H 49 PHE 0.013 0.001 PHE F 58 TRP 0.007 0.001 TRP I 47 HIS 0.004 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 6870) covalent geometry : angle 0.56514 ( 9375) SS BOND : bond 0.00874 ( 6) SS BOND : angle 2.94108 ( 12) hydrogen bonds : bond 0.04630 ( 405) hydrogen bonds : angle 4.01163 ( 1071) link_NAG-ASN : bond 0.00176 ( 3) link_NAG-ASN : angle 1.90658 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1237.30 seconds wall clock time: 22 minutes 7.48 seconds (1327.48 seconds total)