Starting phenix.real_space_refine on Fri Jul 19 06:05:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvh_41642/07_2024/8tvh_41642.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvh_41642/07_2024/8tvh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvh_41642/07_2024/8tvh_41642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvh_41642/07_2024/8tvh_41642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvh_41642/07_2024/8tvh_41642.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvh_41642/07_2024/8tvh_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 Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "I TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C GLU 474": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.05, per 1000 atoms: 0.90 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 - 3.50 Amino acid : False - 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: 2.31 Conformation dependent library (CDL) restraints added in 1.2 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: 0.86 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: 1.89 Time building geometry restraints manager: 2.57 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: 99.01 - 105.97: 164 105.97 - 112.94: 3471 112.94 - 119.90: 2313 119.90 - 126.86: 3364 126.86 - 133.82: 63 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 2.520 nonbonded pdb=" NZ LYS D 39 " pdb=" O GLU D 81 " model vdw 2.491 2.520 nonbonded pdb=" NZ LYS H 39 " pdb=" O GLU H 81 " model vdw 2.492 2.520 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' } 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: 8.790 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.980 Find NCS groups from input model: 0.270 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.077 6870 Z= 0.816 Angle : 1.378 7.951 9375 Z= 0.931 Chirality : 0.081 0.374 1080 Planarity : 0.006 0.022 1230 Dihedral : 12.107 87.727 2331 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.30 % Favored : 97.38 % Rotamer: Outliers : 0.52 % Allowed : 2.95 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.26), residues: 915 helix: 1.99 (0.24), residues: 228 sheet: 1.62 (0.31), residues: 273 loop : 0.10 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.007 TRP G 47 HIS 0.004 0.002 HIS E 30 PHE 0.017 0.004 PHE I 27 TYR 0.026 0.003 TYR E 36 ARG 0.003 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.722 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: 0.2279 time to fit residues: 28.9507 Evaluate side-chains 66 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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: 0.6980 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 H 89 GLN A 157 GLN B 157 GLN C 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6870 Z= 0.276 Angle : 0.626 8.164 9375 Z= 0.325 Chirality : 0.045 0.141 1080 Planarity : 0.004 0.035 1230 Dihedral : 5.135 40.944 1051 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.69 % Allowed : 7.99 % Favored : 91.32 % 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: 2.85 (0.29), residues: 915 helix: 4.67 (0.25), residues: 231 sheet: 1.52 (0.30), residues: 306 loop : 0.43 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 47 HIS 0.002 0.001 HIS G 35 PHE 0.010 0.002 PHE F 58 TYR 0.010 0.001 TYR G 33 ARG 0.001 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.729 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 107 average time/residue: 0.1622 time to fit residues: 24.2073 Evaluate side-chains 85 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 0.0970 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6870 Z= 0.229 Angle : 0.547 7.621 9375 Z= 0.281 Chirality : 0.042 0.132 1080 Planarity : 0.004 0.030 1230 Dihedral : 4.536 29.930 1047 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.04 % Allowed : 12.67 % Favored : 86.28 % 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: 2.95 (0.29), residues: 915 helix: 5.16 (0.26), residues: 228 sheet: 1.40 (0.29), residues: 327 loop : 0.33 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.001 0.000 HIS I 35 PHE 0.012 0.002 PHE F 58 TYR 0.011 0.001 TYR E 49 ARG 0.001 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.516 Fit side-chains REVERT: G 102 THR cc_start: 0.9377 (p) cc_final: 0.9069 (p) REVERT: F 102 THR cc_start: 0.9357 (p) cc_final: 0.9134 (p) REVERT: H 36 TYR cc_start: 0.9370 (m-80) cc_final: 0.9113 (m-80) REVERT: I 102 THR cc_start: 0.9301 (p) cc_final: 0.9072 (p) REVERT: I 114 THR cc_start: 0.8812 (t) cc_final: 0.8590 (t) outliers start: 6 outliers final: 5 residues processed: 103 average time/residue: 0.1717 time to fit residues: 24.5601 Evaluate side-chains 97 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 61 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 6870 Z= 0.464 Angle : 0.663 6.464 9375 Z= 0.345 Chirality : 0.045 0.155 1080 Planarity : 0.005 0.039 1230 Dihedral : 4.948 26.740 1047 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.34 % Allowed : 11.81 % Favored : 83.85 % 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: 2.51 (0.29), residues: 915 helix: 4.55 (0.28), residues: 228 sheet: 1.32 (0.29), residues: 345 loop : -0.03 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 47 HIS 0.004 0.002 HIS G 35 PHE 0.012 0.002 PHE H 98 TYR 0.015 0.002 TYR D 49 ARG 0.003 0.001 ARG A 171 *********************** 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 118 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.955 Fit side-chains REVERT: D 91 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8932 (m-80) REVERT: G 102 THR cc_start: 0.9455 (p) cc_final: 0.9246 (p) REVERT: G 116 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8620 (m) REVERT: F 105 TYR cc_start: 0.9118 (m-80) cc_final: 0.8871 (m-80) REVERT: I 114 THR cc_start: 0.8851 (t) cc_final: 0.8597 (t) REVERT: A 454 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6329 (mt0) outliers start: 25 outliers final: 14 residues processed: 109 average time/residue: 0.1543 time to fit residues: 24.0356 Evaluate side-chains 99 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 116 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 0.0060 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6870 Z= 0.260 Angle : 0.550 7.598 9375 Z= 0.279 Chirality : 0.041 0.131 1080 Planarity : 0.004 0.040 1230 Dihedral : 4.471 23.610 1047 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.47 % Allowed : 12.85 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.05 (0.28), residues: 228 sheet: 1.27 (0.29), residues: 348 loop : -0.02 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 47 HIS 0.002 0.001 HIS E 90 PHE 0.012 0.001 PHE F 58 TYR 0.010 0.001 TYR E 49 ARG 0.001 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.760 Fit side-chains REVERT: D 91 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8777 (m-80) REVERT: G 116 VAL cc_start: 0.8697 (OUTLIER) cc_final: 0.8480 (m) REVERT: F 105 TYR cc_start: 0.9085 (m-80) cc_final: 0.8848 (m-80) REVERT: I 114 THR cc_start: 0.8840 (t) cc_final: 0.8581 (t) REVERT: I 116 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8485 (t) REVERT: A 454 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.5992 (mm-40) outliers start: 20 outliers final: 11 residues processed: 106 average time/residue: 0.1697 time to fit residues: 24.7999 Evaluate side-chains 99 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 G residue 116 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain A residue 454 GLN 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 51 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 6870 Z= 0.422 Angle : 0.639 6.444 9375 Z= 0.328 Chirality : 0.044 0.141 1080 Planarity : 0.005 0.047 1230 Dihedral : 4.691 22.202 1047 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.99 % Allowed : 14.24 % Favored : 81.77 % 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: 2.36 (0.29), residues: 915 helix: 4.60 (0.28), residues: 228 sheet: 1.27 (0.30), residues: 351 loop : -0.34 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 47 HIS 0.004 0.002 HIS H 90 PHE 0.011 0.002 PHE I 27 TYR 0.013 0.002 TYR D 49 ARG 0.003 0.000 ARG C 171 *********************** 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 108 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.756 Fit side-chains REVERT: D 91 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8909 (m-80) REVERT: G 116 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8571 (m) REVERT: F 105 TYR cc_start: 0.9073 (m-80) cc_final: 0.8861 (m-80) REVERT: H 47 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8741 (mp) REVERT: I 114 THR cc_start: 0.8992 (t) cc_final: 0.8732 (t) REVERT: A 454 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6231 (mt0) outliers start: 23 outliers final: 14 residues processed: 101 average time/residue: 0.1607 time to fit residues: 22.8297 Evaluate side-chains 99 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 116 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.6980 chunk 49 optimal weight: 0.0170 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6870 Z= 0.203 Angle : 0.528 8.228 9375 Z= 0.264 Chirality : 0.040 0.132 1080 Planarity : 0.004 0.042 1230 Dihedral : 4.164 18.718 1047 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.30 % Allowed : 15.45 % 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: 2.66 (0.30), residues: 915 helix: 5.21 (0.27), residues: 228 sheet: 1.28 (0.29), residues: 348 loop : -0.23 (0.35), residues: 339 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 0.012 0.001 PHE F 58 TYR 0.009 0.001 TYR E 49 ARG 0.004 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.725 Fit side-chains REVERT: D 91 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8765 (m-80) REVERT: F 105 TYR cc_start: 0.9080 (m-80) cc_final: 0.8875 (m-80) REVERT: I 114 THR cc_start: 0.8982 (t) cc_final: 0.8722 (t) REVERT: I 116 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8483 (t) REVERT: A 454 GLN cc_start: 0.6823 (OUTLIER) cc_final: 0.5879 (mm-40) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 0.1600 time to fit residues: 23.0831 Evaluate side-chains 102 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 116 VAL 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 26 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.0970 chunk 59 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6870 Z= 0.214 Angle : 0.534 7.602 9375 Z= 0.267 Chirality : 0.040 0.133 1080 Planarity : 0.004 0.041 1230 Dihedral : 4.037 17.517 1047 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.30 % Allowed : 16.15 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.30), residues: 915 helix: 5.24 (0.28), residues: 228 sheet: 1.27 (0.29), residues: 348 loop : -0.22 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 47 HIS 0.002 0.001 HIS H 90 PHE 0.012 0.001 PHE F 58 TYR 0.009 0.001 TYR E 49 ARG 0.003 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.765 Fit side-chains REVERT: D 91 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8838 (m-80) REVERT: F 105 TYR cc_start: 0.9090 (m-80) cc_final: 0.8872 (m-80) REVERT: I 114 THR cc_start: 0.9001 (t) cc_final: 0.8719 (t) REVERT: I 116 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8451 (t) REVERT: A 454 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.5904 (mm-40) outliers start: 19 outliers final: 12 residues processed: 97 average time/residue: 0.1627 time to fit residues: 22.2568 Evaluate side-chains 97 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 54 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain A residue 454 GLN 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 80 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 89 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6870 Z= 0.272 Angle : 0.560 7.301 9375 Z= 0.282 Chirality : 0.041 0.137 1080 Planarity : 0.004 0.042 1230 Dihedral : 4.068 15.627 1047 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.30 % Allowed : 15.80 % 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: 2.52 (0.30), residues: 915 helix: 5.06 (0.28), residues: 228 sheet: 1.22 (0.30), residues: 351 loop : -0.32 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 47 HIS 0.003 0.001 HIS E 90 PHE 0.012 0.001 PHE F 58 TYR 0.009 0.001 TYR E 49 ARG 0.003 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.739 Fit side-chains REVERT: D 91 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8815 (m-80) REVERT: F 105 TYR cc_start: 0.9092 (m-80) cc_final: 0.8887 (m-80) REVERT: I 114 THR cc_start: 0.9015 (t) cc_final: 0.8720 (t) REVERT: I 116 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8478 (t) REVERT: A 454 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.5931 (mm-40) outliers start: 19 outliers final: 15 residues processed: 96 average time/residue: 0.1678 time to fit residues: 22.3799 Evaluate side-chains 98 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 54 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain I residue 116 VAL 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 40 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6870 Z= 0.188 Angle : 0.525 7.600 9375 Z= 0.261 Chirality : 0.040 0.130 1080 Planarity : 0.004 0.040 1230 Dihedral : 3.887 15.549 1047 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.95 % Allowed : 16.49 % 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: 2.61 (0.30), residues: 915 helix: 5.32 (0.27), residues: 228 sheet: 1.17 (0.30), residues: 351 loop : -0.28 (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 H 90 PHE 0.014 0.001 PHE F 58 TYR 0.009 0.001 TYR E 49 ARG 0.004 0.000 ARG F 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.748 Fit side-chains REVERT: D 91 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: F 105 TYR cc_start: 0.9092 (m-80) cc_final: 0.8877 (m-80) REVERT: I 114 THR cc_start: 0.8987 (t) cc_final: 0.8726 (t) REVERT: I 116 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8467 (t) REVERT: A 454 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.5815 (mm-40) outliers start: 17 outliers final: 12 residues processed: 100 average time/residue: 0.1555 time to fit residues: 21.7881 Evaluate side-chains 99 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 54 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain I residue 116 VAL 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 65 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 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 = 0.3306 r_free = 0.3306 target = 0.122476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.107591 restraints weight = 8361.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.106093 restraints weight = 8557.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.105997 restraints weight = 9188.550| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6870 Z= 0.304 Angle : 0.576 6.995 9375 Z= 0.291 Chirality : 0.042 0.137 1080 Planarity : 0.004 0.043 1230 Dihedral : 4.019 15.213 1047 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.78 % Allowed : 17.71 % Favored : 79.51 % 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: 2.44 (0.30), residues: 915 helix: 5.00 (0.28), residues: 228 sheet: 1.21 (0.30), residues: 351 loop : -0.42 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 47 HIS 0.004 0.001 HIS H 90 PHE 0.013 0.001 PHE F 58 TYR 0.010 0.002 TYR E 49 ARG 0.003 0.001 ARG F 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.50 seconds wall clock time: 30 minutes 41.60 seconds (1841.60 seconds total)