Starting phenix.real_space_refine on Mon Apr 28 00:13:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvh_41642/04_2025/8tvh_41642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvh_41642/04_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_41642/04_2025/8tvh_41642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvh_41642/04_2025/8tvh_41642.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvh_41642/04_2025/8tvh_41642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvh_41642/04_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-5669/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: 6.83, per 1000 atoms: 1.01 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: 1.73 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.92 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: 2.05 Time building geometry restraints manager: 1.93 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: 4.580 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: 0.060 Set scattering table: 0.070 Process input model: 22.520 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.460 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.06725 ( 3) link_NAG-ASN : angle 5.62580 ( 9) hydrogen bonds : bond 0.18961 ( 405) hydrogen bonds : angle 6.45512 ( 1071) SS BOND : bond 0.09503 ( 6) SS BOND : angle 3.53938 ( 12) covalent geometry : bond 0.01240 ( 6870) covalent geometry : angle 1.37761 ( 9375) *********************** 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 : 0.695 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: 0.2190 time to fit residues: 27.8476 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 : 0.696 ------------------------------------------------------------------------------- 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: 1.9990 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 6879 Z= 0.167 Angle : 0.626 8.208 9396 Z= 0.322 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 3) link_NAG-ASN : angle 1.42405 ( 9) hydrogen bonds : bond 0.06059 ( 405) hydrogen bonds : angle 5.17174 ( 1071) SS BOND : bond 0.01224 ( 6) SS BOND : angle 1.90808 ( 12) covalent geometry : bond 0.00365 ( 6870) covalent geometry : angle 0.62143 ( 9375) *********************** 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 : 0.774 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.1803 time to fit residues: 23.8668 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 : 0.779 ------------------------------------------------------------------------------- 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 6879 Z= 0.192 Angle : 0.602 7.430 9396 Z= 0.311 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 3) link_NAG-ASN : angle 1.32777 ( 9) hydrogen bonds : bond 0.05597 ( 405) hydrogen bonds : angle 4.64668 ( 1071) SS BOND : bond 0.01241 ( 6) SS BOND : angle 2.82591 ( 12) covalent geometry : bond 0.00456 ( 6870) covalent geometry : angle 0.59232 ( 9375) *********************** 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 : 0.640 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: 0.1624 time to fit residues: 23.4021 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 : 0.810 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.127692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.111837 restraints weight = 8411.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.111828 restraints weight = 8391.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.111828 restraints weight = 8368.222| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6879 Z= 0.147 Angle : 0.543 7.687 9396 Z= 0.273 Chirality : 0.041 0.128 1080 Planarity : 0.004 0.033 1230 Dihedral : 4.450 25.987 1047 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.78 % Allowed : 12.50 % 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: 2.91 (0.29), residues: 915 helix: 5.23 (0.27), residues: 228 sheet: 1.19 (0.28), residues: 345 loop : 0.39 (0.36), residues: 342 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 0.009 0.001 TYR E 49 ARG 0.002 0.000 ARG D 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00021 ( 3) link_NAG-ASN : angle 1.36537 ( 9) hydrogen bonds : bond 0.04649 ( 405) hydrogen bonds : angle 4.33776 ( 1071) SS BOND : bond 0.00833 ( 6) SS BOND : angle 2.44374 ( 12) covalent geometry : bond 0.00350 ( 6870) covalent geometry : angle 0.53504 ( 9375) *********************** 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 113 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.782 Fit side-chains REVERT: D 91 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8732 (m-80) REVERT: F 102 THR cc_start: 0.9455 (p) cc_final: 0.9233 (p) REVERT: I 102 THR cc_start: 0.9360 (p) cc_final: 0.9150 (p) REVERT: A 454 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.5946 (mm-40) REVERT: C 473 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7285 (mt-10) outliers start: 16 outliers final: 7 residues processed: 110 average time/residue: 0.1485 time to fit residues: 23.3368 Evaluate side-chains 98 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 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: 0.9990 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: 0.9980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.122005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104339 restraints weight = 8405.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104340 restraints weight = 8093.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104353 restraints weight = 8090.071| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 6879 Z= 0.254 Angle : 0.644 6.369 9396 Z= 0.330 Chirality : 0.044 0.142 1080 Planarity : 0.005 0.040 1230 Dihedral : 4.755 23.846 1047 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.82 % Allowed : 13.02 % Favored : 83.16 % 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: 2.42 (0.29), residues: 915 helix: 4.63 (0.28), residues: 228 sheet: 1.12 (0.29), residues: 351 loop : -0.03 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 47 HIS 0.003 0.001 HIS H 90 PHE 0.011 0.002 PHE I 27 TYR 0.013 0.002 TYR H 49 ARG 0.003 0.001 ARG A 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 3) link_NAG-ASN : angle 1.70933 ( 9) hydrogen bonds : bond 0.05892 ( 405) hydrogen bonds : angle 4.52372 ( 1071) SS BOND : bond 0.01093 ( 6) SS BOND : angle 3.23850 ( 12) covalent geometry : bond 0.00618 ( 6870) covalent geometry : angle 0.63155 ( 9375) *********************** 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 114 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.737 Fit side-chains REVERT: D 91 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8957 (m-80) REVERT: F 105 TYR cc_start: 0.9118 (m-80) cc_final: 0.8900 (m-80) REVERT: I 114 THR cc_start: 0.9129 (t) cc_final: 0.8916 (t) REVERT: A 454 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6328 (mm-40) outliers start: 22 outliers final: 12 residues processed: 107 average time/residue: 0.1728 time to fit residues: 25.5272 Evaluate side-chains 101 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 86 LEU 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 A residue 454 GLN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C 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: 0.9990 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 78 optimal weight: 0.0060 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.138553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.119011 restraints weight = 8176.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119742 restraints weight = 7619.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.119909 restraints weight = 7256.890| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4159 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= 0.163 Angle : 0.562 7.090 9396 Z= 0.283 Chirality : 0.041 0.134 1080 Planarity : 0.004 0.040 1230 Dihedral : 4.423 21.069 1047 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.30 % Allowed : 14.06 % 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: 2.62 (0.29), residues: 915 helix: 4.92 (0.28), residues: 231 sheet: 1.25 (0.29), residues: 348 loop : -0.07 (0.36), 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 0.011 0.001 PHE F 58 TYR 0.010 0.001 TYR E 49 ARG 0.002 0.000 ARG B 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00016 ( 3) link_NAG-ASN : angle 1.66631 ( 9) hydrogen bonds : bond 0.04924 ( 405) hydrogen bonds : angle 4.25417 ( 1071) SS BOND : bond 0.00862 ( 6) SS BOND : angle 2.50230 ( 12) covalent geometry : bond 0.00388 ( 6870) covalent geometry : angle 0.55347 ( 9375) *********************** 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 109 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.809 Fit side-chains REVERT: D 91 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8772 (m-80) REVERT: F 105 TYR cc_start: 0.9074 (m-80) cc_final: 0.8844 (m-80) REVERT: I 114 THR cc_start: 0.9098 (t) cc_final: 0.8851 (t) REVERT: A 454 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6070 (mm-40) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 0.1661 time to fit residues: 23.8465 Evaluate side-chains 100 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.124778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109795 restraints weight = 8239.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109795 restraints weight = 8302.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109795 restraints weight = 8302.163| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4359 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= 0.148 Angle : 0.548 6.746 9396 Z= 0.274 Chirality : 0.041 0.131 1080 Planarity : 0.004 0.040 1230 Dihedral : 4.174 18.609 1047 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.60 % Allowed : 15.80 % Favored : 81.60 % 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: 2.66 (0.30), residues: 915 helix: 5.07 (0.28), residues: 231 sheet: 1.23 (0.29), residues: 348 loop : -0.10 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.002 0.001 HIS H 90 PHE 0.010 0.001 PHE F 58 TYR 0.009 0.001 TYR E 49 ARG 0.003 0.000 ARG C 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 3) link_NAG-ASN : angle 1.74703 ( 9) hydrogen bonds : bond 0.04493 ( 405) hydrogen bonds : angle 4.01178 ( 1071) SS BOND : bond 0.00861 ( 6) SS BOND : angle 2.34336 ( 12) covalent geometry : bond 0.00352 ( 6870) covalent geometry : angle 0.53922 ( 9375) *********************** 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 106 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.757 Fit side-chains REVERT: D 91 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8824 (m-80) REVERT: G 108 ASP cc_start: 0.8088 (t70) cc_final: 0.7837 (t0) REVERT: A 454 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.5933 (mm-40) outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 0.1618 time to fit residues: 22.9596 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 : 0.733 ------------------------------------------------------------------------------- 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 45 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 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 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.151663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.135386 restraints weight = 7772.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.136154 restraints weight = 7244.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.136154 restraints weight = 6801.387| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4468 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 : 0.567 6.740 9396 Z= 0.285 Chirality : 0.042 0.132 1080 Planarity : 0.004 0.041 1230 Dihedral : 4.130 16.352 1047 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.60 % Allowed : 16.15 % 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 (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: 2.55 (0.30), residues: 915 helix: 4.95 (0.28), residues: 231 sheet: 1.22 (0.29), residues: 348 loop : -0.23 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 47 HIS 0.003 0.001 HIS E 90 PHE 0.011 0.001 PHE F 58 TYR 0.009 0.001 TYR E 49 ARG 0.002 0.000 ARG C 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 3) link_NAG-ASN : angle 1.85749 ( 9) hydrogen bonds : bond 0.04769 ( 405) hydrogen bonds : angle 4.08391 ( 1071) SS BOND : bond 0.00805 ( 6) SS BOND : angle 2.52795 ( 12) covalent geometry : bond 0.00399 ( 6870) covalent geometry : angle 0.55733 ( 9375) *********************** 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 98 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.712 Fit side-chains REVERT: D 91 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8800 (m-80) REVERT: A 454 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6022 (mm-40) outliers start: 15 outliers final: 12 residues processed: 92 average time/residue: 0.1572 time to fit residues: 20.5112 Evaluate side-chains 93 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 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 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.0170 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5756 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.124489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.109499 restraints weight = 8341.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.108460 restraints weight = 9037.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.108412 restraints weight = 9525.176| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6879 Z= 0.144 Angle : 0.553 7.110 9396 Z= 0.275 Chirality : 0.041 0.134 1080 Planarity : 0.004 0.040 1230 Dihedral : 4.005 15.688 1047 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.60 % Allowed : 16.49 % Favored : 80.90 % 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: 2.61 (0.30), residues: 915 helix: 5.09 (0.28), residues: 231 sheet: 1.26 (0.30), residues: 348 loop : -0.25 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 47 HIS 0.002 0.001 HIS H 90 PHE 0.013 0.001 PHE F 58 TYR 0.009 0.001 TYR E 49 ARG 0.002 0.000 ARG C 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00035 ( 3) link_NAG-ASN : angle 1.83239 ( 9) hydrogen bonds : bond 0.04434 ( 405) hydrogen bonds : angle 3.97785 ( 1071) SS BOND : bond 0.00718 ( 6) SS BOND : angle 2.41693 ( 12) covalent geometry : bond 0.00340 ( 6870) covalent geometry : angle 0.54336 ( 9375) *********************** 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 94 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.793 Fit side-chains REVERT: D 91 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8818 (m-80) REVERT: A 454 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.5947 (mm-40) outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 0.1651 time to fit residues: 20.8563 Evaluate side-chains 92 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 56 ASP 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 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 63 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 78 optimal weight: 0.0170 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.126375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.111375 restraints weight = 8369.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.111375 restraints weight = 8369.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.111375 restraints weight = 8369.965| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6879 Z= 0.123 Angle : 0.534 7.337 9396 Z= 0.266 Chirality : 0.040 0.131 1080 Planarity : 0.004 0.038 1230 Dihedral : 3.924 16.664 1047 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.43 % Allowed : 17.01 % 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: 2.68 (0.30), residues: 915 helix: 5.25 (0.28), residues: 231 sheet: 1.17 (0.30), residues: 351 loop : -0.14 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.003 0.001 HIS H 90 PHE 0.013 0.001 PHE F 58 TYR 0.009 0.001 TYR E 49 ARG 0.002 0.000 ARG C 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 3) link_NAG-ASN : angle 1.78355 ( 9) hydrogen bonds : bond 0.04019 ( 405) hydrogen bonds : angle 3.88704 ( 1071) SS BOND : bond 0.00690 ( 6) SS BOND : angle 2.41107 ( 12) covalent geometry : bond 0.00284 ( 6870) covalent geometry : angle 0.52489 ( 9375) ********************** 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 102 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.735 Fit side-chains REVERT: D 91 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: A 454 GLN cc_start: 0.6792 (OUTLIER) cc_final: 0.5827 (mm-40) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.1656 time to fit residues: 22.8232 Evaluate side-chains 94 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 56 ASP Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 0.0060 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.150050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.133993 restraints weight = 7864.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.134784 restraints weight = 7281.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134990 restraints weight = 6877.596| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6879 Z= 0.194 Angle : 0.597 6.976 9396 Z= 0.300 Chirality : 0.042 0.138 1080 Planarity : 0.004 0.040 1230 Dihedral : 4.049 16.884 1047 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.78 % Allowed : 17.53 % 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: 2.45 (0.30), residues: 915 helix: 4.87 (0.28), residues: 231 sheet: 1.22 (0.30), residues: 351 loop : -0.37 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 47 HIS 0.003 0.001 HIS E 90 PHE 0.013 0.001 PHE F 58 TYR 0.010 0.002 TYR D 49 ARG 0.002 0.000 ARG C 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 2.01846 ( 9) hydrogen bonds : bond 0.04974 ( 405) hydrogen bonds : angle 4.10871 ( 1071) SS BOND : bond 0.00899 ( 6) SS BOND : angle 2.83618 ( 12) covalent geometry : bond 0.00473 ( 6870) covalent geometry : angle 0.58603 ( 9375) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.95 seconds wall clock time: 43 minutes 31.98 seconds (2611.98 seconds total)