Starting phenix.real_space_refine on Sat May 10 18:29:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvh_41642/05_2025/8tvh_41642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvh_41642/05_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_41642/05_2025/8tvh_41642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvh_41642/05_2025/8tvh_41642.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvh_41642/05_2025/8tvh_41642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvh_41642/05_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.53, per 1000 atoms: 0.82 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: 1.55 Conformation dependent library (CDL) restraints added in 1.0 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: 0.90 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: 1.85 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: 6.830 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 19.960 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- 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 : 0.680 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: 0.2246 time to fit residues: 28.5021 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 : 0.719 ------------------------------------------------------------------------------- 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 = 65)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112795 restraints weight = 8322.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.113419 restraints weight = 7648.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.113960 restraints weight = 7212.565| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 1.42406 ( 9) hydrogen bonds : bond 0.06059 ( 405) hydrogen bonds : angle 5.17174 ( 1071) SS BOND : bond 0.01223 ( 6) SS BOND : angle 1.90810 ( 12) covalent geometry : bond 0.00365 ( 6870) covalent geometry : angle 0.62144 ( 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 : 0.684 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.1612 time to fit residues: 21.5565 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 : 0.655 ------------------------------------------------------------------------------- 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: 0.5980 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.128131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.107189 restraints weight = 8579.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.107321 restraints weight = 8161.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.107326 restraints weight = 8003.994| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6879 Z= 0.169 Angle : 0.582 7.579 9396 Z= 0.299 Chirality : 0.042 0.136 1080 Planarity : 0.004 0.033 1230 Dihedral : 4.628 30.739 1047 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.26 % Allowed : 11.63 % 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: 2.79 (0.29), residues: 915 helix: 5.05 (0.26), residues: 228 sheet: 1.30 (0.29), residues: 327 loop : 0.24 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 47 HIS 0.002 0.000 HIS I 35 PHE 0.011 0.002 PHE F 58 TYR 0.012 0.002 TYR E 49 ARG 0.001 0.000 ARG C 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 3) link_NAG-ASN : angle 1.32456 ( 9) hydrogen bonds : bond 0.05239 ( 405) hydrogen bonds : angle 4.55878 ( 1071) SS BOND : bond 0.01032 ( 6) SS BOND : angle 2.51158 ( 12) covalent geometry : bond 0.00392 ( 6870) covalent geometry : angle 0.57429 ( 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 110 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.734 Fit side-chains REVERT: G 102 THR cc_start: 0.9398 (p) cc_final: 0.9097 (p) REVERT: F 102 THR cc_start: 0.9392 (p) cc_final: 0.9155 (p) REVERT: I 102 THR cc_start: 0.9330 (p) cc_final: 0.9092 (p) REVERT: I 114 THR cc_start: 0.8963 (t) cc_final: 0.8643 (t) outliers start: 13 outliers final: 8 residues processed: 103 average time/residue: 0.1586 time to fit residues: 22.9331 Evaluate side-chains 98 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 F residue 70 ILE 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: 1.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 0.0050 chunk 76 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.127152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.108958 restraints weight = 8420.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109214 restraints weight = 7996.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109214 restraints weight = 7756.618| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6879 Z= 0.157 Angle : 0.551 7.919 9396 Z= 0.278 Chirality : 0.042 0.134 1080 Planarity : 0.004 0.032 1230 Dihedral : 4.445 25.314 1047 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.60 % Allowed : 12.50 % Favored : 84.90 % 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: 2.87 (0.29), residues: 915 helix: 5.19 (0.27), residues: 228 sheet: 1.38 (0.29), residues: 327 loop : 0.18 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 47 HIS 0.002 0.000 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 0.00101 ( 3) link_NAG-ASN : angle 1.35852 ( 9) hydrogen bonds : bond 0.04748 ( 405) hydrogen bonds : angle 4.34274 ( 1071) SS BOND : bond 0.00917 ( 6) SS BOND : angle 2.55335 ( 12) covalent geometry : bond 0.00374 ( 6870) covalent geometry : angle 0.54212 ( 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 111 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.667 Fit side-chains REVERT: D 91 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8751 (m-80) REVERT: G 102 THR cc_start: 0.9449 (p) cc_final: 0.9242 (p) REVERT: F 102 THR cc_start: 0.9457 (p) cc_final: 0.9243 (p) REVERT: I 102 THR cc_start: 0.9377 (p) cc_final: 0.9166 (p) REVERT: A 454 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.5998 (mm-40) REVERT: C 473 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7304 (mt-10) outliers start: 15 outliers final: 6 residues processed: 107 average time/residue: 0.1431 time to fit residues: 21.8395 Evaluate side-chains 99 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 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: 0.0970 chunk 13 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 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: 0.7778 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.134401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.114078 restraints weight = 8317.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.114078 restraints weight = 7792.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.114078 restraints weight = 7792.473| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6879 Z= 0.181 Angle : 0.571 6.911 9396 Z= 0.290 Chirality : 0.042 0.134 1080 Planarity : 0.004 0.034 1230 Dihedral : 4.421 22.629 1047 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.47 % Allowed : 13.54 % Favored : 82.99 % 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: 2.69 (0.29), residues: 915 helix: 5.03 (0.28), residues: 228 sheet: 1.16 (0.28), residues: 348 loop : 0.15 (0.36), residues: 339 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 H 49 ARG 0.002 0.000 ARG A 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 3) link_NAG-ASN : angle 1.51007 ( 9) hydrogen bonds : bond 0.04999 ( 405) hydrogen bonds : angle 4.28377 ( 1071) SS BOND : bond 0.00976 ( 6) SS BOND : angle 2.68553 ( 12) covalent geometry : bond 0.00437 ( 6870) covalent geometry : angle 0.56117 ( 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 117 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.725 Fit side-chains REVERT: D 91 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: F 105 TYR cc_start: 0.9095 (m-80) cc_final: 0.8838 (m-80) REVERT: I 114 THR cc_start: 0.9094 (t) cc_final: 0.8799 (t) REVERT: A 454 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6113 (mm-40) REVERT: C 473 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7371 (mt-10) outliers start: 20 outliers final: 12 residues processed: 112 average time/residue: 0.1689 time to fit residues: 25.9401 Evaluate side-chains 104 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 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 A residue 454 GLN 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: 0.6980 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.123658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.107373 restraints weight = 8414.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.106302 restraints weight = 8820.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.106314 restraints weight = 9383.913| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6879 Z= 0.178 Angle : 0.567 7.078 9396 Z= 0.287 Chirality : 0.041 0.134 1080 Planarity : 0.004 0.036 1230 Dihedral : 4.366 20.639 1047 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.12 % Allowed : 14.41 % Favored : 82.47 % 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: 2.65 (0.29), residues: 915 helix: 4.94 (0.28), residues: 231 sheet: 1.36 (0.29), residues: 327 loop : -0.07 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 47 HIS 0.003 0.001 HIS H 90 PHE 0.011 0.001 PHE F 58 TYR 0.009 0.001 TYR D 49 ARG 0.001 0.000 ARG E 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 3) link_NAG-ASN : angle 1.59996 ( 9) hydrogen bonds : bond 0.04926 ( 405) hydrogen bonds : angle 4.22365 ( 1071) SS BOND : bond 0.00881 ( 6) SS BOND : angle 2.65555 ( 12) covalent geometry : bond 0.00429 ( 6870) covalent geometry : angle 0.55751 ( 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 104 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.598 Fit side-chains REVERT: D 91 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8819 (m-80) REVERT: F 105 TYR cc_start: 0.9085 (m-80) cc_final: 0.8849 (m-80) REVERT: I 114 THR cc_start: 0.9086 (t) cc_final: 0.8839 (t) REVERT: A 454 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6052 (mm-40) REVERT: C 473 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7369 (mt-10) outliers start: 18 outliers final: 9 residues processed: 97 average time/residue: 0.1590 time to fit residues: 21.6626 Evaluate side-chains 96 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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=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: 0.9980 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.159044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.141520 restraints weight = 7667.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.142597 restraints weight = 6862.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.143065 restraints weight = 6371.692| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4270 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 : 0.561 7.007 9396 Z= 0.281 Chirality : 0.041 0.132 1080 Planarity : 0.004 0.036 1230 Dihedral : 4.248 18.424 1047 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.43 % Allowed : 15.28 % 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: 2.67 (0.29), residues: 915 helix: 4.99 (0.28), residues: 231 sheet: 1.22 (0.29), residues: 348 loop : 0.01 (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 H 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 0.00094 ( 3) link_NAG-ASN : angle 1.68823 ( 9) hydrogen bonds : bond 0.04768 ( 405) hydrogen bonds : angle 4.14341 ( 1071) SS BOND : bond 0.00853 ( 6) SS BOND : angle 2.56432 ( 12) covalent geometry : bond 0.00401 ( 6870) covalent geometry : angle 0.55118 ( 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 103 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.731 Fit side-chains REVERT: D 91 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8816 (m-80) REVERT: F 105 TYR cc_start: 0.9079 (m-80) cc_final: 0.8834 (m-80) REVERT: I 114 THR cc_start: 0.9063 (t) cc_final: 0.8800 (t) REVERT: A 454 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6016 (mm-40) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.1621 time to fit residues: 22.2280 Evaluate side-chains 99 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain F residue 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 479 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: 1.9990 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.123448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.108149 restraints weight = 8408.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.107014 restraints weight = 8560.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.106872 restraints weight = 9107.382| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4386 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= 0.168 Angle : 0.562 6.759 9396 Z= 0.282 Chirality : 0.041 0.133 1080 Planarity : 0.004 0.037 1230 Dihedral : 4.145 15.955 1047 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.95 % Allowed : 15.10 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.56 (0.29), residues: 915 helix: 4.97 (0.28), residues: 231 sheet: 1.09 (0.29), residues: 351 loop : -0.06 (0.36), 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 0.011 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 0.00112 ( 3) link_NAG-ASN : angle 1.82782 ( 9) hydrogen bonds : bond 0.04749 ( 405) hydrogen bonds : angle 4.13051 ( 1071) SS BOND : bond 0.00871 ( 6) SS BOND : angle 2.53057 ( 12) covalent geometry : bond 0.00403 ( 6870) covalent geometry : angle 0.55220 ( 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 105 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.675 Fit side-chains REVERT: D 91 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: A 454 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6014 (mm-40) outliers start: 17 outliers final: 11 residues processed: 99 average time/residue: 0.1488 time to fit residues: 20.9992 Evaluate side-chains 97 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 E residue 104 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.153725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.137865 restraints weight = 7795.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138021 restraints weight = 7224.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.138526 restraints weight = 7056.677| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6879 Z= 0.139 Angle : 0.543 7.062 9396 Z= 0.271 Chirality : 0.041 0.132 1080 Planarity : 0.004 0.038 1230 Dihedral : 4.015 15.189 1047 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.60 % Allowed : 15.45 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.60 (0.30), residues: 915 helix: 5.14 (0.29), residues: 231 sheet: 1.05 (0.29), residues: 351 loop : -0.06 (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 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 0.00023 ( 3) link_NAG-ASN : angle 1.79376 ( 9) hydrogen bonds : bond 0.04380 ( 405) hydrogen bonds : angle 4.00926 ( 1071) SS BOND : bond 0.00778 ( 6) SS BOND : angle 2.30415 ( 12) covalent geometry : bond 0.00329 ( 6870) covalent geometry : angle 0.53400 ( 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 100 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.692 Fit side-chains REVERT: D 91 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8777 (m-80) REVERT: A 454 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.5970 (mm-40) outliers start: 15 outliers final: 11 residues processed: 94 average time/residue: 0.1469 time to fit residues: 19.9113 Evaluate side-chains 95 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 E residue 104 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain 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: 0.6980 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.149840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132910 restraints weight = 7970.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133658 restraints weight = 7245.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133801 restraints weight = 6796.077| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6879 Z= 0.148 Angle : 0.551 6.874 9396 Z= 0.275 Chirality : 0.041 0.134 1080 Planarity : 0.004 0.038 1230 Dihedral : 3.973 15.070 1047 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: 2.57 (0.30), residues: 915 helix: 5.10 (0.28), residues: 231 sheet: 1.09 (0.29), residues: 351 loop : -0.14 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.00081 ( 3) link_NAG-ASN : angle 1.85890 ( 9) hydrogen bonds : bond 0.04431 ( 405) hydrogen bonds : angle 4.00671 ( 1071) SS BOND : bond 0.00759 ( 6) SS BOND : angle 2.49693 ( 12) covalent geometry : bond 0.00353 ( 6870) covalent geometry : angle 0.54152 ( 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 100 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.703 Fit side-chains REVERT: D 91 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8824 (m-80) REVERT: A 454 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.5986 (mm-40) outliers start: 15 outliers final: 11 residues processed: 94 average time/residue: 0.1621 time to fit residues: 22.0494 Evaluate side-chains 96 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 E residue 104 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain I residue 114 THR 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 47 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 86 optimal weight: 0.0470 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 0.0000 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 overall best weight: 0.3482 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.127163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.112135 restraints weight = 8386.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.112135 restraints weight = 8379.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.112135 restraints weight = 8379.794| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6879 Z= 0.115 Angle : 0.525 7.336 9396 Z= 0.261 Chirality : 0.040 0.130 1080 Planarity : 0.004 0.038 1230 Dihedral : 3.879 16.018 1047 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.43 % Allowed : 16.67 % 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: 2.66 (0.30), residues: 915 helix: 5.33 (0.28), residues: 231 sheet: 1.03 (0.29), residues: 351 loop : -0.05 (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 H 90 PHE 0.014 0.001 PHE F 58 TYR 0.008 0.001 TYR E 49 ARG 0.002 0.000 ARG C 171 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 3) link_NAG-ASN : angle 1.75393 ( 9) hydrogen bonds : bond 0.03833 ( 405) hydrogen bonds : angle 3.85731 ( 1071) SS BOND : bond 0.00734 ( 6) SS BOND : angle 2.30638 ( 12) covalent geometry : bond 0.00260 ( 6870) covalent geometry : angle 0.51590 ( 9375) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2317.86 seconds wall clock time: 41 minutes 27.59 seconds (2487.59 seconds total)