Starting phenix.real_space_refine on Fri Mar 15 11:55:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6s_36013/03_2024/8j6s_36013.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6s_36013/03_2024/8j6s_36013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6s_36013/03_2024/8j6s_36013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6s_36013/03_2024/8j6s_36013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6s_36013/03_2024/8j6s_36013.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6s_36013/03_2024/8j6s_36013.pdb" } resolution = 3.8 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1568 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 197 5.49 5 S 15 5.16 5 C 5640 2.51 5 N 1918 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 53": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10030 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 484 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 83 Chain: "H" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 468 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 1, 'TRANS': 69} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 663 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 482 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "I" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2009 Classifications: {'DNA': 99} Link IDs: {'rna3p': 98} Chain: "C" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 676 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 85} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 571 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 568 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 510 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 67} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2031 Classifications: {'DNA': 98} Link IDs: {'rna3p': 97} Chain: "L" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 1494 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 264} Link IDs: {'PTRANS': 9, 'TRANS': 292} Chain breaks: 7 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 962 Unresolved non-hydrogen angles: 1252 Unresolved non-hydrogen dihedrals: 822 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 15, 'TYR:plan': 11, 'ASN:plan1': 12, 'TRP:plan': 8, 'ASP:plan': 20, 'PHE:plan': 16, 'GLU:plan': 11, 'HIS:plan': 10} Unresolved non-hydrogen planarities: 534 Chain: "K" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 74 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 14} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 5.90, per 1000 atoms: 0.59 Number of scatterers: 10030 At special positions: 0 Unit cell: (103, 114, 113, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 197 15.00 O 2260 8.00 N 1918 7.00 C 5640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 1.3 seconds 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 53.2% alpha, 12.3% beta 90 base pairs and 149 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.716A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 removed outlier: 3.570A pdb=" N ALA G 114 " --> pdb=" O CYS G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 132 removed outlier: 3.800A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 29 removed outlier: 3.556A pdb=" N ILE H 29 " --> pdb=" O ILE H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 49 through 76 removed outlier: 4.098A pdb=" N ARG H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN H 64 " --> pdb=" O VAL H 60 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'E' and resid 46 through 57 removed outlier: 4.225A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.392A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.942A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.684A pdb=" N SER C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.564A pdb=" N PHE C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 30 through 42 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.514A pdb=" N ARG D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.864A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.829A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.557A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 704 through 708 Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.940A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84 removed outlier: 7.016A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'L' and resid 2 through 6 removed outlier: 3.949A pdb=" N CYS L 370 " --> pdb=" O CYS L 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 18 through 21 removed outlier: 3.658A pdb=" N SER L 18 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA L 35 " --> pdb=" O SER L 18 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LYS L 45 " --> pdb=" O PHE L 58 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE L 58 " --> pdb=" O LYS L 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 74 removed outlier: 5.850A pdb=" N LYS L 94 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL L 121 " --> pdb=" O LYS L 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 132 through 137 removed outlier: 6.409A pdb=" N ALA L 153 " --> pdb=" O ILE L 166 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE L 166 " --> pdb=" O ALA L 153 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE L 155 " --> pdb=" O ILE L 164 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN L 162 " --> pdb=" O ASP L 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 174 through 179 removed outlier: 6.438A pdb=" N LEU L 195 " --> pdb=" O ASN L 208 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN L 208 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL L 197 " --> pdb=" O ALA L 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 241 through 242 removed outlier: 4.223A pdb=" N ALA L 279 " --> pdb=" O VAL L 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 290 through 293 removed outlier: 3.751A pdb=" N SER L 342 " --> pdb=" O VAL K 684 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL K 684 " --> pdb=" O SER L 342 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 225 hydrogen bonds 434 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 149 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2473 1.34 - 1.46: 2881 1.46 - 1.58: 4782 1.58 - 1.70: 392 1.70 - 1.82: 23 Bond restraints: 10551 Sorted by residual: bond pdb=" CB MET E 120 " pdb=" CG MET E 120 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.39e+00 bond pdb=" CB PRO B 32 " pdb=" CG PRO B 32 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.87e+00 bond pdb=" C3' DC J 75 " pdb=" O3' DC J 75 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB GLN E 68 " pdb=" CG GLN E 68 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB PRO C 66 " pdb=" CG PRO C 66 " ideal model delta sigma weight residual 1.492 1.553 -0.061 5.00e-02 4.00e+02 1.49e+00 ... (remaining 10546 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.00: 829 105.00 - 112.00: 5741 112.00 - 119.00: 2812 119.00 - 126.00: 5179 126.00 - 133.00: 620 Bond angle restraints: 15181 Sorted by residual: angle pdb=" CA PRO C 66 " pdb=" N PRO C 66 " pdb=" CD PRO C 66 " ideal model delta sigma weight residual 112.00 103.82 8.18 1.40e+00 5.10e-01 3.42e+01 angle pdb=" CA PRO G 121 " pdb=" N PRO G 121 " pdb=" CD PRO G 121 " ideal model delta sigma weight residual 112.00 104.18 7.82 1.40e+00 5.10e-01 3.12e+01 angle pdb=" CA ARG B 36 " pdb=" CB ARG B 36 " pdb=" CG ARG B 36 " ideal model delta sigma weight residual 114.10 123.36 -9.26 2.00e+00 2.50e-01 2.14e+01 angle pdb=" CB MET E 120 " pdb=" CG MET E 120 " pdb=" SD MET E 120 " ideal model delta sigma weight residual 112.70 125.32 -12.62 3.00e+00 1.11e-01 1.77e+01 angle pdb=" CA ARG B 92 " pdb=" CB ARG B 92 " pdb=" CG ARG B 92 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.51e+01 ... (remaining 15176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 4721 34.83 - 69.65: 1009 69.65 - 104.48: 49 104.48 - 139.31: 0 139.31 - 174.13: 4 Dihedral angle restraints: 5783 sinusoidal: 3085 harmonic: 2698 Sorted by residual: dihedral pdb=" CA MET G 120 " pdb=" C MET G 120 " pdb=" N PRO G 121 " pdb=" CA PRO G 121 " ideal model delta harmonic sigma weight residual 180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ARG A 63 " pdb=" C ARG A 63 " pdb=" N LYS A 64 " pdb=" CA LYS A 64 " ideal model delta harmonic sigma weight residual -180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ARG G 63 " pdb=" C ARG G 63 " pdb=" N LYS G 64 " pdb=" CA LYS G 64 " ideal model delta harmonic sigma weight residual -180.00 -158.80 -21.20 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 5780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1486 0.050 - 0.099: 270 0.099 - 0.149: 67 0.149 - 0.199: 7 0.199 - 0.249: 3 Chirality restraints: 1833 Sorted by residual: chirality pdb=" CA PRO C 66 " pdb=" N PRO C 66 " pdb=" C PRO C 66 " pdb=" CB PRO C 66 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO G 121 " pdb=" N PRO G 121 " pdb=" C PRO G 121 " pdb=" CB PRO G 121 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1830 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET G 120 " -0.087 5.00e-02 4.00e+02 1.26e-01 2.56e+01 pdb=" N PRO G 121 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO G 121 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO G 121 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 65 " -0.074 5.00e-02 4.00e+02 1.07e-01 1.85e+01 pdb=" N PRO C 66 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO C 66 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 66 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.057 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO B 32 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.047 5.00e-02 4.00e+02 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 55 2.51 - 3.10: 7159 3.10 - 3.70: 18366 3.70 - 4.30: 23082 4.30 - 4.90: 33522 Nonbonded interactions: 82184 Sorted by model distance: nonbonded pdb=" NH2 ARG A 63 " pdb=" C5' DA J 33 " model vdw 1.907 3.520 nonbonded pdb=" O2 DC I 56 " pdb=" N2 DG J 92 " model vdw 2.068 2.496 nonbonded pdb=" OG1 THR H 30 " pdb=" OP1 DC I 36 " model vdw 2.098 2.440 nonbonded pdb=" O2 DC I 66 " pdb=" N2 DG J 82 " model vdw 2.104 2.496 nonbonded pdb=" OG1 THR D 80 " pdb=" OP1 DC J 75 " model vdw 2.110 2.440 ... (remaining 82179 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' and ((resid 59 through 60 and (name N or name CA or name C or name O \ or name CB )) or resid 61 through 63 or (resid 64 through 65 and (name N or name \ CA or name C or name O or name CB )) or resid 66 or (resid 67 through 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 104 or (r \ esid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 t \ hrough 124 or (resid 125 and (name N or name CA or name C or name O or name CB ) \ ) or resid 126 through 133)) selection = (chain 'C' and ((resid 59 through 60 and (name N or name CA or name C or name O \ or name CB )) or resid 61 through 63 or (resid 64 through 65 and (name N or name \ CA or name C or name O or name CB )) or resid 66 or (resid 67 through 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 124 or (r \ esid 125 and (name N or name CA or name C or name O or name CB )) or resid 126 t \ hrough 132 or (resid 133 and (name N or name CA or name C or name O or name CB ) \ ))) selection = chain 'G' } ncs_group { reference = (chain 'B' and ((resid 26 through 27 and (name N or name CA or name C or name O \ or name CB )) or resid 28 or (resid 29 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 34 or (resid 35 and (name N or na \ me CA or name C or name O or name CB )) or resid 36 through 38 or (resid 39 thro \ ugh 40 and (name N or name CA or name C or name O or name CB )) or resid 41 thro \ ugh 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or \ resid 45 through 48 or (resid 49 and (name N or name CA or name C or name O or n \ ame CB )) or resid 50 through 51 or (resid 52 through 55 and (name N or name CA \ or name C or name O or name CB )) or resid 56 through 63 or (resid 64 and (name \ N or name CA or name C or name O or name CB )) or resid 65 or (resid 66 through \ 85 and (name N or name CA or name C or name O or name CB )) or resid 86 through \ 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or resi \ d 92 through 94)) selection = (chain 'D' and ((resid 26 through 27 and (name N or name CA or name C or name O \ or name CB )) or resid 28 or (resid 29 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 34 or (resid 35 and (name N or na \ me CA or name C or name O or name CB )) or resid 36 through 38 or (resid 39 thro \ ugh 40 and (name N or name CA or name C or name O or name CB )) or resid 41 thro \ ugh 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or \ resid 45 through 48 or (resid 49 and (name N or name CA or name C or name O or n \ ame CB )) or resid 50 through 52 or (resid 53 through 55 and (name N or name CA \ or name C or name O or name CB )) or resid 56 through 58 or (resid 59 and (name \ N or name CA or name C or name O or name CB )) or resid 60 through 62 or (resid \ 63 through 64 and (name N or name CA or name C or name O or name CB )) or resid \ 65 or (resid 66 through 85 and (name N or name CA or name C or name O or name CB \ )) or resid 86 through 90 or (resid 91 and (name N or name CA or name C or name \ O or name CB )) or resid 92 through 94)) selection = (chain 'F' and (resid 26 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 38 or (resid 39 through 40 and (na \ me N or name CA or name C or name O or name CB )) or resid 41 through 52 or (res \ id 53 through 55 and (name N or name CA or name C or name O or name CB )) or res \ id 56 through 63 or (resid 64 and (name N or name CA or name C or name O or name \ CB )) or resid 65 or (resid 66 through 85 and (name N or name CA or name C or n \ ame O or name CB )) or resid 86 through 94)) selection = (chain 'H' and ((resid 26 through 30 and (name N or name CA or name C or name O \ or name CB )) or resid 31 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 48 or (resid 49 and (name N or na \ me CA or name C or name O or name CB )) or resid 50 through 71 or (resid 72 thro \ ugh 85 and (name N or name CA or name C or name O or name CB )) or resid 86 thro \ ugh 94)) } 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 4.590 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 33.880 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.004 0.068 10551 Z= 0.249 Angle : 0.795 12.621 15181 Z= 0.456 Chirality : 0.044 0.249 1833 Planarity : 0.007 0.126 1279 Dihedral : 29.579 174.135 4015 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.06 % Allowed : 38.36 % Favored : 60.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.27), residues: 897 helix: 0.23 (0.23), residues: 457 sheet: 1.13 (0.47), residues: 126 loop : -1.51 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.013 0.004 HIS D 75 PHE 0.022 0.002 PHE E 84 TYR 0.044 0.002 TYR H 72 ARG 0.015 0.001 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8508 (ttp80) REVERT: E 97 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8020 (mm-30) REVERT: E 130 ILE cc_start: 0.8796 (tp) cc_final: 0.8119 (tp) REVERT: E 131 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7980 (mtp180) REVERT: C 51 ILE cc_start: 0.8959 (mp) cc_final: 0.8346 (mp) REVERT: C 93 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 59 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8582 (tppp) REVERT: D 60 VAL cc_start: 0.9102 (t) cc_final: 0.8865 (p) REVERT: A 90 MET cc_start: 0.8099 (tmt) cc_final: 0.7265 (tmm) outliers start: 4 outliers final: 1 residues processed: 200 average time/residue: 0.2784 time to fit residues: 71.9855 Evaluate side-chains 151 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 84 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 50.0000 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 97 optimal weight: 50.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10551 Z= 0.236 Angle : 0.702 9.177 15181 Z= 0.395 Chirality : 0.041 0.231 1833 Planarity : 0.005 0.061 1279 Dihedral : 31.375 179.753 3123 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.35 % Allowed : 31.75 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.27), residues: 897 helix: 0.57 (0.23), residues: 468 sheet: 1.12 (0.47), residues: 127 loop : -1.26 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.009 0.003 HIS H 75 PHE 0.014 0.002 PHE C 104 TYR 0.029 0.002 TYR H 72 ARG 0.011 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 90 LEU cc_start: 0.9600 (mt) cc_final: 0.9388 (pp) REVERT: H 92 ARG cc_start: 0.8874 (mtp-110) cc_final: 0.8592 (ttp80) REVERT: H 93 GLN cc_start: 0.9292 (tp40) cc_final: 0.8970 (tm-30) REVERT: F 88 TYR cc_start: 0.8049 (m-80) cc_final: 0.7780 (m-80) REVERT: C 50 GLU cc_start: 0.8559 (tt0) cc_final: 0.8333 (mp0) REVERT: D 59 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8598 (mmmm) REVERT: D 63 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7335 (mm-30) REVERT: A 90 MET cc_start: 0.8166 (tmt) cc_final: 0.6778 (tmm) REVERT: A 94 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7745 (mm-30) outliers start: 24 outliers final: 10 residues processed: 178 average time/residue: 0.2519 time to fit residues: 60.1533 Evaluate side-chains 149 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 20.0000 chunk 80 optimal weight: 50.0000 chunk 66 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 105 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 50.0000 overall best weight: 4.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 10551 Z= 0.371 Angle : 0.736 9.800 15181 Z= 0.417 Chirality : 0.043 0.315 1833 Planarity : 0.005 0.057 1279 Dihedral : 31.864 179.902 3121 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 7.67 % Allowed : 34.66 % Favored : 57.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.27), residues: 897 helix: 0.58 (0.23), residues: 471 sheet: 1.02 (0.48), residues: 125 loop : -1.21 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.005 0.002 HIS H 75 PHE 0.021 0.002 PHE C 84 TYR 0.025 0.002 TYR H 72 ARG 0.011 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 90 LEU cc_start: 0.9624 (mt) cc_final: 0.9213 (tt) REVERT: H 92 ARG cc_start: 0.8853 (mtp-110) cc_final: 0.8528 (ttp80) REVERT: H 93 GLN cc_start: 0.9382 (tp40) cc_final: 0.9059 (tm-30) REVERT: F 88 TYR cc_start: 0.8188 (m-80) cc_final: 0.7820 (m-80) REVERT: D 59 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8535 (tppp) REVERT: D 63 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7210 (mm-30) REVERT: D 67 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7846 (ttm-80) REVERT: A 90 MET cc_start: 0.8214 (tmt) cc_final: 0.6722 (tmm) REVERT: A 94 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7947 (mm-30) outliers start: 29 outliers final: 22 residues processed: 163 average time/residue: 0.2489 time to fit residues: 54.3582 Evaluate side-chains 148 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 30.0000 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 50.0000 chunk 103 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 40.0000 chunk 27 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10551 Z= 0.269 Angle : 0.714 10.898 15181 Z= 0.394 Chirality : 0.041 0.269 1833 Planarity : 0.005 0.061 1279 Dihedral : 31.734 178.550 3121 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 8.99 % Allowed : 35.45 % Favored : 55.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.27), residues: 897 helix: 0.79 (0.23), residues: 469 sheet: 0.98 (0.48), residues: 125 loop : -1.10 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.004 0.002 HIS H 75 PHE 0.017 0.002 PHE C 104 TYR 0.020 0.002 TYR H 72 ARG 0.009 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 ARG cc_start: 0.8859 (mtp-110) cc_final: 0.8581 (ttp80) REVERT: H 93 GLN cc_start: 0.9353 (tp40) cc_final: 0.9040 (tm-30) REVERT: F 88 TYR cc_start: 0.8129 (m-80) cc_final: 0.7694 (m-80) REVERT: D 59 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8469 (tppp) REVERT: A 90 MET cc_start: 0.8185 (tmt) cc_final: 0.6804 (tmm) REVERT: A 94 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7799 (mm-30) REVERT: B 55 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8660 (ttm-80) outliers start: 34 outliers final: 21 residues processed: 163 average time/residue: 0.2636 time to fit residues: 56.5926 Evaluate side-chains 153 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 92 optimal weight: 40.0000 chunk 26 optimal weight: 1.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10551 Z= 0.295 Angle : 0.724 13.142 15181 Z= 0.398 Chirality : 0.042 0.359 1833 Planarity : 0.005 0.057 1279 Dihedral : 31.811 178.512 3121 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 8.47 % Allowed : 37.04 % Favored : 54.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.27), residues: 897 helix: 0.91 (0.23), residues: 469 sheet: 0.92 (0.49), residues: 121 loop : -1.08 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.005 0.002 HIS G 113 PHE 0.019 0.002 PHE C 84 TYR 0.019 0.001 TYR H 72 ARG 0.009 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 MET cc_start: 0.7737 (pmm) cc_final: 0.7504 (pmm) REVERT: H 93 GLN cc_start: 0.9370 (tp40) cc_final: 0.9166 (tm-30) REVERT: E 97 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7967 (mm-30) REVERT: F 88 TYR cc_start: 0.8163 (m-80) cc_final: 0.7767 (m-80) REVERT: D 59 LYS cc_start: 0.9113 (mmmm) cc_final: 0.8694 (tptm) REVERT: A 90 MET cc_start: 0.8148 (tmt) cc_final: 0.6771 (tmm) REVERT: A 94 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7809 (mm-30) REVERT: B 55 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8708 (mmt90) REVERT: B 67 ARG cc_start: 0.9275 (mmm160) cc_final: 0.8887 (mmm160) outliers start: 32 outliers final: 25 residues processed: 159 average time/residue: 0.2547 time to fit residues: 53.8377 Evaluate side-chains 155 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 6.9990 chunk 93 optimal weight: 50.0000 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 99 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 10551 Z= 0.279 Angle : 0.730 10.790 15181 Z= 0.398 Chirality : 0.041 0.347 1833 Planarity : 0.005 0.095 1279 Dihedral : 31.801 177.434 3121 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 7.67 % Allowed : 39.42 % Favored : 52.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.27), residues: 897 helix: 1.02 (0.23), residues: 469 sheet: 0.85 (0.48), residues: 121 loop : -1.08 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.004 0.001 HIS H 75 PHE 0.021 0.002 PHE G 104 TYR 0.017 0.001 TYR H 72 ARG 0.008 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 GLN cc_start: 0.9460 (tp40) cc_final: 0.9130 (tp-100) REVERT: E 97 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8024 (mm-30) REVERT: F 88 TYR cc_start: 0.8224 (m-80) cc_final: 0.7829 (m-80) REVERT: D 59 LYS cc_start: 0.9135 (mmmm) cc_final: 0.8761 (tptm) REVERT: A 94 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8059 (mm-30) REVERT: B 55 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8693 (mmt90) REVERT: B 67 ARG cc_start: 0.9245 (mmm160) cc_final: 0.8911 (mmm160) outliers start: 29 outliers final: 21 residues processed: 157 average time/residue: 0.2464 time to fit residues: 52.0835 Evaluate side-chains 153 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 40.0000 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10551 Z= 0.225 Angle : 0.742 13.444 15181 Z= 0.395 Chirality : 0.041 0.344 1833 Planarity : 0.005 0.053 1279 Dihedral : 31.623 175.608 3121 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 7.41 % Allowed : 41.53 % Favored : 51.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.27), residues: 897 helix: 0.96 (0.23), residues: 471 sheet: 0.97 (0.48), residues: 117 loop : -0.89 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.005 0.002 HIS G 113 PHE 0.041 0.003 PHE A 67 TYR 0.017 0.001 TYR H 72 ARG 0.011 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 MET cc_start: 0.7530 (pmm) cc_final: 0.7264 (pmm) REVERT: H 93 GLN cc_start: 0.9450 (tp40) cc_final: 0.9147 (tp-100) REVERT: F 88 TYR cc_start: 0.8182 (m-80) cc_final: 0.7737 (m-80) REVERT: D 59 LYS cc_start: 0.9041 (mmmm) cc_final: 0.8706 (tptm) REVERT: A 90 MET cc_start: 0.8087 (tmt) cc_final: 0.6884 (tmm) REVERT: A 94 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7939 (mm-30) REVERT: A 129 ARG cc_start: 0.7561 (ttm110) cc_final: 0.7337 (ptm160) REVERT: B 55 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8544 (mmt90) REVERT: B 67 ARG cc_start: 0.9262 (mmm160) cc_final: 0.8943 (mmm160) outliers start: 28 outliers final: 21 residues processed: 162 average time/residue: 0.2371 time to fit residues: 52.2673 Evaluate side-chains 155 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 50.0000 chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 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 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10551 Z= 0.203 Angle : 0.748 14.212 15181 Z= 0.396 Chirality : 0.041 0.376 1833 Planarity : 0.004 0.048 1279 Dihedral : 31.315 173.064 3121 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.29 % Allowed : 43.65 % Favored : 51.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.28), residues: 897 helix: 0.93 (0.24), residues: 476 sheet: 0.99 (0.48), residues: 119 loop : -0.79 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.005 0.002 HIS G 113 PHE 0.043 0.002 PHE A 67 TYR 0.017 0.001 TYR H 72 ARG 0.008 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 GLN cc_start: 0.9422 (tp40) cc_final: 0.9137 (tp-100) REVERT: E 120 MET cc_start: 0.7633 (mmm) cc_final: 0.7328 (mtt) REVERT: F 88 TYR cc_start: 0.8116 (m-80) cc_final: 0.7663 (m-80) REVERT: D 59 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8106 (tptm) REVERT: D 60 VAL cc_start: 0.9033 (p) cc_final: 0.8604 (m) REVERT: D 63 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7086 (mp0) REVERT: A 90 MET cc_start: 0.7947 (tmt) cc_final: 0.6839 (tmm) REVERT: A 94 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 55 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8587 (mmt90) REVERT: B 66 ILE cc_start: 0.9533 (pt) cc_final: 0.9212 (pt) REVERT: B 67 ARG cc_start: 0.9304 (mmm160) cc_final: 0.8896 (mmm160) outliers start: 20 outliers final: 13 residues processed: 161 average time/residue: 0.2543 time to fit residues: 54.7714 Evaluate side-chains 149 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 50.0000 chunk 96 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 95 optimal weight: 30.0000 chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 10551 Z= 0.341 Angle : 0.785 14.849 15181 Z= 0.425 Chirality : 0.043 0.323 1833 Planarity : 0.005 0.054 1279 Dihedral : 31.827 177.586 3121 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.29 % Allowed : 45.77 % Favored : 48.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.27), residues: 897 helix: 0.69 (0.23), residues: 476 sheet: 1.11 (0.47), residues: 117 loop : -0.90 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.004 0.001 HIS G 113 PHE 0.050 0.003 PHE A 67 TYR 0.016 0.001 TYR D 51 ARG 0.008 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 GLN cc_start: 0.9457 (tp40) cc_final: 0.9140 (tp-100) REVERT: F 88 TYR cc_start: 0.8190 (m-80) cc_final: 0.7794 (m-80) REVERT: C 54 TYR cc_start: 0.8591 (m-80) cc_final: 0.8301 (m-80) REVERT: D 59 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8880 (tptm) REVERT: A 92 LEU cc_start: 0.8706 (pp) cc_final: 0.8394 (pp) REVERT: B 55 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8710 (mmt90) REVERT: B 67 ARG cc_start: 0.9299 (mmm160) cc_final: 0.9017 (mmm160) outliers start: 20 outliers final: 15 residues processed: 151 average time/residue: 0.2506 time to fit residues: 50.6257 Evaluate side-chains 146 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 106 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 chunk 84 optimal weight: 50.0000 chunk 8 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 90 optimal weight: 50.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 10551 Z= 0.352 Angle : 0.814 15.456 15181 Z= 0.439 Chirality : 0.043 0.304 1833 Planarity : 0.006 0.088 1279 Dihedral : 32.076 175.011 3121 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 27.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.23 % Allowed : 47.62 % Favored : 48.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.27), residues: 897 helix: 0.56 (0.23), residues: 476 sheet: 0.96 (0.47), residues: 119 loop : -0.84 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.004 0.001 HIS G 113 PHE 0.050 0.002 PHE A 67 TYR 0.016 0.001 TYR D 51 ARG 0.013 0.001 ARG A 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 GLN cc_start: 0.9435 (tp40) cc_final: 0.9136 (tp-100) REVERT: F 88 TYR cc_start: 0.8184 (m-80) cc_final: 0.7885 (m-80) REVERT: C 54 TYR cc_start: 0.8679 (m-80) cc_final: 0.8450 (m-80) REVERT: C 55 GLN cc_start: 0.8571 (mt0) cc_final: 0.8313 (mp10) REVERT: D 59 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8925 (tptm) REVERT: A 90 MET cc_start: 0.7862 (tmt) cc_final: 0.7330 (tmm) REVERT: A 92 LEU cc_start: 0.8642 (pp) cc_final: 0.8253 (pp) REVERT: A 129 ARG cc_start: 0.7686 (ttm110) cc_final: 0.7364 (ptm160) REVERT: B 67 ARG cc_start: 0.9311 (mmm160) cc_final: 0.9014 (mmm160) outliers start: 16 outliers final: 14 residues processed: 142 average time/residue: 0.2404 time to fit residues: 46.5582 Evaluate side-chains 139 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 50.0000 chunk 12 optimal weight: 50.0000 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 40.0000 chunk 35 optimal weight: 5.9990 chunk 87 optimal weight: 40.0000 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** 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 = 0.3429 r_free = 0.3429 target = 0.049835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.034467 restraints weight = 76510.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.035492 restraints weight = 43448.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.036176 restraints weight = 30303.673| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 10551 Z= 0.286 Angle : 0.808 16.733 15181 Z= 0.428 Chirality : 0.043 0.384 1833 Planarity : 0.005 0.071 1279 Dihedral : 31.992 173.323 3121 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 24.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.76 % Allowed : 47.09 % Favored : 48.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.27), residues: 897 helix: 0.61 (0.23), residues: 475 sheet: 1.04 (0.46), residues: 117 loop : -0.86 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.005 0.002 HIS G 113 PHE 0.052 0.002 PHE A 67 TYR 0.015 0.001 TYR H 72 ARG 0.013 0.001 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1888.59 seconds wall clock time: 34 minutes 42.75 seconds (2082.75 seconds total)