Starting phenix.real_space_refine on Tue Mar 11 21:31:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvh_41642/03_2025/8tvh_41642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvh_41642/03_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_41642/03_2025/8tvh_41642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvh_41642/03_2025/8tvh_41642.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvh_41642/03_2025/8tvh_41642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvh_41642/03_2025/8tvh_41642.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN: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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN: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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN: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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 4, '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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 4, '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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 4, '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: 5.22, per 1000 atoms: 0.77 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: 1.64 Conformation dependent library (CDL) restraints added in 997.0 milliseconds 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: 0.96 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: 1.92 Time building geometry restraints manager: 1.95 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: 0.05 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 'C' selection = chain 'B' } 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: 4.420 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.120 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.650 ------------------------------------------------------------------------------- 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 : 0.012 0.077 6870 Z= 0.816 Angle : 1.378 7.951 9375 Z= 0.931 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.028 0.007 TRP G 47 HIS 0.004 0.002 HIS E 30 PHE 0.017 0.004 PHE I 27 TYR 0.026 0.003 TYR E 36 ARG 0.003 0.001 ARG D 61 *********************** 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 : 0.690 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: 0.2193 time to fit residues: 27.8888 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 : 0.741 ------------------------------------------------------------------------------- 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 75 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.133781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112827 restraints weight = 8322.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112827 restraints weight = 7638.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112827 restraints weight = 7638.689| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6870 Z= 0.243 Angle : 0.621 8.208 9375 Z= 0.320 Chirality : 0.044 0.152 1080 Planarity : 0.004 0.035 1230 Dihedral : 5.098 40.889 1051 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.52 % Allowed : 7.81 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.29), residues: 915 helix: 4.76 (0.25), residues: 231 sheet: 1.54 (0.30), residues: 306 loop : 0.41 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 47 HIS 0.001 0.001 HIS I 35 PHE 0.011 0.001 PHE F 58 TYR 0.009 0.001 TYR I 60 ARG 0.003 0.000 ARG E 96 *********************** 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 98 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.737 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.1660 time to fit residues: 22.1811 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 : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 47 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.126475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.105424 restraints weight = 8610.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.105426 restraints weight = 8163.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.105426 restraints weight = 8161.370| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6870 Z= 0.300 Angle : 0.592 7.430 9375 Z= 0.307 Chirality : 0.043 0.137 1080 Planarity : 0.004 0.032 1230 Dihedral : 4.735 30.865 1047 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.91 % Allowed : 11.98 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.29), residues: 915 helix: 4.91 (0.26), residues: 228 sheet: 1.31 (0.29), residues: 327 loop : 0.20 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 47 HIS 0.002 0.001 HIS I 35 PHE 0.012 0.002 PHE F 58 TYR 0.012 0.002 TYR E 49 ARG 0.002 0.000 ARG C 171 *********************** 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 109 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.679 Fit side-chains REVERT: G 102 THR cc_start: 0.9404 (p) cc_final: 0.9136 (p) REVERT: F 102 THR cc_start: 0.9394 (p) cc_final: 0.9160 (p) REVERT: I 102 THR cc_start: 0.9338 (p) cc_final: 0.9113 (p) REVERT: I 114 THR cc_start: 0.8984 (t) cc_final: 0.8668 (t) outliers start: 11 outliers final: 7 residues processed: 103 average time/residue: 0.1633 time to fit residues: 23.6235 Evaluate side-chains 97 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 54 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 Chi-restraints excluded: chain H residue 45 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 0.0270 chunk 66 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.127241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109191 restraints weight = 8408.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109191 restraints weight = 8053.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109191 restraints weight = 8052.841| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6870 Z= 0.255 Angle : 0.545 7.620 9375 Z= 0.277 Chirality : 0.041 0.130 1080 Planarity : 0.004 0.032 1230 Dihedral : 4.508 26.185 1047 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.95 % Allowed : 12.33 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.29), residues: 915 helix: 5.15 (0.27), residues: 228 sheet: 1.31 (0.29), residues: 330 loop : 0.17 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 47 HIS 0.002 0.001 HIS G 35 PHE 0.011 0.001 PHE F 58 TYR 0.010 0.001 TYR E 49 ARG 0.002 0.000 ARG D 96 *********************** 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 114 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.784 Fit side-chains REVERT: D 91 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8758 (m-80) REVERT: F 102 THR cc_start: 0.9463 (p) cc_final: 0.9242 (p) REVERT: I 102 THR cc_start: 0.9368 (p) cc_final: 0.9163 (p) REVERT: A 454 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6032 (mm-40) REVERT: C 473 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7298 (mt-10) outliers start: 17 outliers final: 9 residues processed: 109 average time/residue: 0.1496 time to fit residues: 23.3567 Evaluate side-chains 101 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 F residue 22 CYS Chi-restraints excluded: chain H residue 91 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.102358 restraints weight = 8457.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.102358 restraints weight = 8174.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.102358 restraints weight = 8174.412| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 6870 Z= 0.472 Angle : 0.681 7.490 9375 Z= 0.353 Chirality : 0.046 0.145 1080 Planarity : 0.005 0.043 1230 Dihedral : 5.039 23.634 1047 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.51 % Allowed : 12.85 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.29), residues: 915 helix: 4.31 (0.28), residues: 228 sheet: 1.17 (0.29), residues: 351 loop : -0.25 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 47 HIS 0.003 0.002 HIS H 90 PHE 0.012 0.002 PHE I 27 TYR 0.014 0.002 TYR D 49 ARG 0.004 0.001 ARG A 171 *********************** 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 117 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.711 Fit side-chains REVERT: D 91 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.9004 (m-80) REVERT: I 114 THR cc_start: 0.9160 (t) cc_final: 0.8947 (t) REVERT: A 454 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6391 (mt0) outliers start: 26 outliers final: 14 residues processed: 110 average time/residue: 0.1695 time to fit residues: 25.5030 Evaluate side-chains 97 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN 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 D residue 104 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 114 THR 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 22 CYS Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 170 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 53 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.150488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134094 restraints weight = 7786.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134256 restraints weight = 7267.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134256 restraints weight = 7085.445| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6870 Z= 0.301 Angle : 0.579 7.024 9375 Z= 0.294 Chirality : 0.042 0.136 1080 Planarity : 0.004 0.044 1230 Dihedral : 4.616 20.766 1047 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.12 % Allowed : 14.58 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.30), residues: 915 helix: 4.80 (0.28), residues: 228 sheet: 1.24 (0.29), residues: 348 loop : -0.38 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 47 HIS 0.003 0.001 HIS E 90 PHE 0.010 0.001 PHE F 58 TYR 0.010 0.001 TYR E 49 ARG 0.005 0.001 ARG G 40 *********************** 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 100 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.715 Fit side-chains REVERT: D 91 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8883 (m-80) REVERT: I 114 THR cc_start: 0.9141 (t) cc_final: 0.8875 (t) REVERT: A 454 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6155 (mm-40) outliers start: 18 outliers final: 11 residues processed: 95 average time/residue: 0.1606 time to fit residues: 21.4312 Evaluate side-chains 94 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 A residue 454 GLN Chi-restraints excluded: chain B residue 170 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 72 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.150976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.135331 restraints weight = 7656.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.135479 restraints weight = 7280.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.135485 restraints weight = 7145.169| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 6870 Z= 0.431 Angle : 0.647 7.025 9375 Z= 0.331 Chirality : 0.044 0.142 1080 Planarity : 0.005 0.048 1230 Dihedral : 4.741 21.693 1047 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.99 % Allowed : 14.93 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.29), residues: 915 helix: 4.45 (0.28), residues: 228 sheet: 1.11 (0.29), residues: 351 loop : -0.65 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 47 HIS 0.005 0.002 HIS H 90 PHE 0.010 0.002 PHE F 58 TYR 0.012 0.002 TYR D 49 ARG 0.003 0.001 ARG G 40 *********************** 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: 23 poor density : 86 time to evaluate : 0.761 Fit side-chains REVERT: D 91 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8983 (m-80) REVERT: I 114 THR cc_start: 0.9195 (t) cc_final: 0.8932 (t) REVERT: A 454 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6302 (mt0) outliers start: 23 outliers final: 18 residues processed: 103 average time/residue: 0.1663 time to fit residues: 23.6925 Evaluate side-chains 101 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 89 GLN Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain E residue 104 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 86 LEU Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 114 THR 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 20 LEU Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.153413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.137537 restraints weight = 7735.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.138112 restraints weight = 7172.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138249 restraints weight = 6799.662| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6870 Z= 0.279 Angle : 0.575 7.866 9375 Z= 0.289 Chirality : 0.042 0.134 1080 Planarity : 0.004 0.045 1230 Dihedral : 4.387 16.965 1047 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.47 % Allowed : 16.32 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.30), residues: 915 helix: 4.88 (0.28), residues: 228 sheet: 1.08 (0.30), residues: 351 loop : -0.62 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 47 HIS 0.003 0.001 HIS H 90 PHE 0.012 0.001 PHE F 58 TYR 0.010 0.001 TYR E 49 ARG 0.004 0.001 ARG G 40 *********************** 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 99 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.708 Fit side-chains REVERT: D 91 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8962 (m-80) REVERT: A 454 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6086 (mm-40) outliers start: 20 outliers final: 15 residues processed: 93 average time/residue: 0.1563 time to fit residues: 20.6620 Evaluate side-chains 96 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 LEU 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 E residue 104 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 F residue 114 THR 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 A residue 454 GLN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.0020 chunk 54 optimal weight: 2.9990 chunk 74 optimal weight: 0.0770 overall best weight: 0.5148 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.123681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.108801 restraints weight = 8376.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.107576 restraints weight = 8439.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.107463 restraints weight = 9043.134| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6870 Z= 0.212 Angle : 0.540 7.764 9375 Z= 0.269 Chirality : 0.041 0.131 1080 Planarity : 0.004 0.042 1230 Dihedral : 4.093 15.390 1047 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.30 % Allowed : 16.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.30), residues: 915 helix: 5.20 (0.28), residues: 228 sheet: 1.09 (0.30), residues: 351 loop : -0.57 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.003 0.001 HIS E 90 PHE 0.013 0.001 PHE F 58 TYR 0.009 0.001 TYR E 49 ARG 0.004 0.000 ARG G 40 *********************** 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 104 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.715 Fit side-chains REVERT: A 454 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.5916 (mm-40) outliers start: 19 outliers final: 15 residues processed: 99 average time/residue: 0.1722 time to fit residues: 23.6844 Evaluate side-chains 95 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 LEU 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 E residue 104 LEU Chi-restraints excluded: chain D residue 54 LEU 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 F residue 114 THR 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 A residue 454 GLN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.105524 restraints weight = 8532.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.104409 restraints weight = 9078.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.104343 restraints weight = 9723.697| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6870 Z= 0.323 Angle : 0.592 7.399 9375 Z= 0.299 Chirality : 0.042 0.136 1080 Planarity : 0.004 0.045 1230 Dihedral : 4.171 16.770 1047 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.95 % Allowed : 17.36 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.30), residues: 915 helix: 4.88 (0.28), residues: 228 sheet: 1.12 (0.30), residues: 351 loop : -0.68 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 47 HIS 0.004 0.001 HIS E 90 PHE 0.013 0.001 PHE F 58 TYR 0.010 0.002 TYR E 49 ARG 0.004 0.001 ARG G 40 ********************** 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 99 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.829 Fit side-chains REVERT: A 454 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6104 (mm-40) outliers start: 17 outliers final: 15 residues processed: 95 average time/residue: 0.1655 time to fit residues: 22.0046 Evaluate side-chains 97 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain G residue 20 LEU 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 89 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 47 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 86 optimal weight: 0.0040 chunk 26 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 5 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 overall best weight: 0.3028 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.125251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.110470 restraints weight = 8415.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109390 restraints weight = 8468.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.109280 restraints weight = 8929.393| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6870 Z= 0.168 Angle : 0.524 8.162 9375 Z= 0.260 Chirality : 0.040 0.129 1080 Planarity : 0.004 0.039 1230 Dihedral : 3.912 15.312 1047 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.95 % Allowed : 17.36 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.30), residues: 915 helix: 5.25 (0.28), residues: 231 sheet: 1.07 (0.30), residues: 351 loop : -0.48 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.002 0.001 HIS E 90 PHE 0.015 0.001 PHE F 58 TYR 0.009 0.001 TYR E 49 ARG 0.004 0.001 ARG F 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2269.14 seconds wall clock time: 39 minutes 59.42 seconds (2399.42 seconds total)