Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 23:55:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg0_30348/04_2023/7cg0_30348.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg0_30348/04_2023/7cg0_30348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg0_30348/04_2023/7cg0_30348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg0_30348/04_2023/7cg0_30348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg0_30348/04_2023/7cg0_30348.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg0_30348/04_2023/7cg0_30348.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.066 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 55 5.16 5 C 6791 2.51 5 N 1925 2.21 5 O 2157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "g PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 117": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10928 Number of models: 1 Model: "" Number of chains: 21 Chain: "0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "2" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "3" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "4" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "5" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "6" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "7" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "9" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "f" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 936 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Chain: "g" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 949 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain breaks: 1 Chain: "h" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 935 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Chain: "j" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 931 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain breaks: 1 Chain: "l" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "m" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "o" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 856 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain breaks: 1 Chain: "p" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 940 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Chain: "8" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "i" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 944 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Chain: "k" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 852 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "n" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 844 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Time building chain proxies: 5.83, per 1000 atoms: 0.53 Number of scatterers: 10928 At special positions: 0 Unit cell: (108.481, 111.095, 129.393, 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 55 16.00 O 2157 8.00 N 1925 7.00 C 6791 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: 4.63 Conformation dependent library (CDL) restraints added in 1.7 seconds 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2798 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 17 sheets defined 53.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'f' and resid 4 through 30 removed outlier: 4.061A pdb=" N ASP f 8 " --> pdb=" O LEU f 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 33 No H-bonds generated for 'chain 'f' and resid 31 through 33' Processing helix chain 'f' and resid 97 through 130 removed outlier: 3.782A pdb=" N LEU f 130 " --> pdb=" O MET f 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 30 removed outlier: 3.881A pdb=" N ASP g 8 " --> pdb=" O LEU g 4 " (cutoff:3.500A) Processing helix chain 'g' and resid 36 through 40 removed outlier: 3.670A pdb=" N GLN g 40 " --> pdb=" O PRO g 37 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 130 removed outlier: 3.742A pdb=" N LEU g 130 " --> pdb=" O MET g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 134 removed outlier: 4.142A pdb=" N GLN g 134 " --> pdb=" O THR g 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 131 through 134' Processing helix chain 'h' and resid 4 through 30 removed outlier: 4.252A pdb=" N ASP h 8 " --> pdb=" O LEU h 4 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 130 removed outlier: 3.927A pdb=" N MET h 106 " --> pdb=" O MET h 102 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 30 removed outlier: 4.042A pdb=" N PHE j 7 " --> pdb=" O LEU j 3 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP j 8 " --> pdb=" O LEU j 4 " (cutoff:3.500A) Processing helix chain 'j' and resid 31 through 33 No H-bonds generated for 'chain 'j' and resid 31 through 33' Processing helix chain 'j' and resid 98 through 131 removed outlier: 3.548A pdb=" N MET j 106 " --> pdb=" O MET j 102 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR j 131 " --> pdb=" O LEU j 127 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 32 removed outlier: 3.614A pdb=" N LEU l 9 " --> pdb=" O LEU l 5 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE l 11 " --> pdb=" O ALA l 7 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLN l 12 " --> pdb=" O ALA l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 44 through 54 Processing helix chain 'l' and resid 101 through 133 Processing helix chain 'm' and resid 4 through 32 removed outlier: 4.607A pdb=" N GLN m 12 " --> pdb=" O ALA m 8 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 54 Processing helix chain 'm' and resid 102 through 134 removed outlier: 3.693A pdb=" N VAL m 133 " --> pdb=" O GLY m 129 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU m 134 " --> pdb=" O MET m 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 32 removed outlier: 4.665A pdb=" N GLN o 12 " --> pdb=" O ALA o 8 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA o 15 " --> pdb=" O PHE o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 44 through 55 Processing helix chain 'o' and resid 101 through 134 removed outlier: 3.716A pdb=" N VAL o 133 " --> pdb=" O GLY o 129 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU o 134 " --> pdb=" O MET o 130 " (cutoff:3.500A) Processing helix chain 'p' and resid 4 through 30 removed outlier: 4.033A pdb=" N ASP p 8 " --> pdb=" O LEU p 4 " (cutoff:3.500A) Processing helix chain 'p' and resid 36 through 40 removed outlier: 3.867A pdb=" N GLN p 40 " --> pdb=" O PRO p 37 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 131 Processing helix chain 'i' and resid 4 through 30 removed outlier: 4.178A pdb=" N ASP i 8 " --> pdb=" O LEU i 4 " (cutoff:3.500A) Processing helix chain 'i' and resid 97 through 130 Processing helix chain 'k' and resid 3 through 32 removed outlier: 3.993A pdb=" N ALA k 8 " --> pdb=" O ARG k 4 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU k 9 " --> pdb=" O LEU k 5 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE k 11 " --> pdb=" O ALA k 7 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLN k 12 " --> pdb=" O ALA k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 44 through 53 Processing helix chain 'k' and resid 102 through 134 removed outlier: 3.613A pdb=" N LEU k 134 " --> pdb=" O MET k 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 32 removed outlier: 4.340A pdb=" N GLN n 12 " --> pdb=" O ALA n 8 " (cutoff:3.500A) Processing helix chain 'n' and resid 44 through 55 removed outlier: 3.612A pdb=" N VAL n 54 " --> pdb=" O LYS n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 134 removed outlier: 3.751A pdb=" N LEU n 134 " --> pdb=" O MET n 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '5' and resid 316 through 317 Processing sheet with id=AA2, first strand: chain '6' and resid 316 through 317 Processing sheet with id=AA3, first strand: chain '7' and resid 316 through 317 Processing sheet with id=AA4, first strand: chain '9' and resid 316 through 317 Processing sheet with id=AA5, first strand: chain 'f' and resid 45 through 52 removed outlier: 6.255A pdb=" N GLN f 46 " --> pdb=" O VAL f 67 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL f 67 " --> pdb=" O GLN f 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL f 48 " --> pdb=" O ALA f 65 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY f 61 " --> pdb=" O ASP f 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 75 through 78 Processing sheet with id=AA7, first strand: chain 'g' and resid 45 through 51 removed outlier: 4.237A pdb=" N VAL g 48 " --> pdb=" O SER g 66 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER g 66 " --> pdb=" O VAL g 48 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLN g 50 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL g 64 " --> pdb=" O GLN g 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 75 through 78 Processing sheet with id=AA9, first strand: chain 'h' and resid 45 through 51 removed outlier: 6.315A pdb=" N GLN h 46 " --> pdb=" O VAL h 67 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL h 67 " --> pdb=" O GLN h 46 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL h 48 " --> pdb=" O ALA h 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'h' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'j' and resid 45 through 51 removed outlier: 4.042A pdb=" N SER j 66 " --> pdb=" O VAL j 48 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN j 50 " --> pdb=" O VAL j 64 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL j 64 " --> pdb=" O GLN j 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'j' and resid 76 through 78 Processing sheet with id=AB4, first strand: chain 'p' and resid 45 through 51 removed outlier: 6.348A pdb=" N GLN p 46 " --> pdb=" O VAL p 67 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL p 67 " --> pdb=" O GLN p 46 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL p 48 " --> pdb=" O ALA p 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'p' and resid 75 through 78 Processing sheet with id=AB6, first strand: chain 'i' and resid 45 through 51 removed outlier: 6.231A pdb=" N GLN i 46 " --> pdb=" O VAL i 67 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL i 67 " --> pdb=" O GLN i 46 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL i 48 " --> pdb=" O ALA i 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'i' and resid 76 through 78 Processing sheet with id=AB8, first strand: chain 'n' and resid 41 through 42 653 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2506 1.33 - 1.45: 1919 1.45 - 1.57: 6508 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 11043 Sorted by residual: bond pdb=" N SER 7 317 " pdb=" CA SER 7 317 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.26e-02 6.30e+03 9.20e+00 bond pdb=" N ASN 7 318 " pdb=" CA ASN 7 318 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.49e+00 bond pdb=" N MET f 125 " pdb=" CA MET f 125 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.33e+00 bond pdb=" N GLN 7 319 " pdb=" CA GLN 7 319 " ideal model delta sigma weight residual 1.452 1.493 -0.040 1.80e-02 3.09e+03 5.04e+00 bond pdb=" N LYS h 128 " pdb=" CA LYS h 128 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 4.98e+00 ... (remaining 11038 not shown) Histogram of bond angle deviations from ideal: 99.78 - 105.56: 326 105.56 - 111.35: 4757 111.35 - 117.13: 2936 117.13 - 122.92: 6294 122.92 - 128.70: 669 Bond angle restraints: 14982 Sorted by residual: angle pdb=" N PRO 7 320 " pdb=" CA PRO 7 320 " pdb=" C PRO 7 320 " ideal model delta sigma weight residual 111.34 117.75 -6.41 1.55e+00 4.16e-01 1.71e+01 angle pdb=" N ASN 7 318 " pdb=" CA ASN 7 318 " pdb=" C ASN 7 318 " ideal model delta sigma weight residual 111.28 115.54 -4.26 1.09e+00 8.42e-01 1.53e+01 angle pdb=" C SER 7 317 " pdb=" N ASN 7 318 " pdb=" CA ASN 7 318 " ideal model delta sigma weight residual 120.28 125.13 -4.85 1.34e+00 5.57e-01 1.31e+01 angle pdb=" CA ASN 7 318 " pdb=" C ASN 7 318 " pdb=" O ASN 7 318 " ideal model delta sigma weight residual 120.55 116.88 3.67 1.06e+00 8.90e-01 1.20e+01 angle pdb=" C PRO 7 320 " pdb=" CA PRO 7 320 " pdb=" CB PRO 7 320 " ideal model delta sigma weight residual 111.12 106.95 4.17 1.29e+00 6.01e-01 1.05e+01 ... (remaining 14977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6481 17.85 - 35.70: 311 35.70 - 53.55: 61 53.55 - 71.40: 8 71.40 - 89.25: 6 Dihedral angle restraints: 6867 sinusoidal: 2575 harmonic: 4292 Sorted by residual: dihedral pdb=" CA VAL i 34 " pdb=" C VAL i 34 " pdb=" N THR i 35 " pdb=" CA THR i 35 " ideal model delta harmonic sigma weight residual 180.00 163.85 16.15 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASN i 22 " pdb=" CB ASN i 22 " pdb=" CG ASN i 22 " pdb=" OD1 ASN i 22 " ideal model delta sinusoidal sigma weight residual -90.00 -157.41 67.41 2 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" N LEU o 18 " pdb=" CA LEU o 18 " pdb=" CB LEU o 18 " pdb=" CG LEU o 18 " ideal model delta sinusoidal sigma weight residual -60.00 -118.68 58.68 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1118 0.030 - 0.059: 466 0.059 - 0.089: 128 0.089 - 0.118: 66 0.118 - 0.148: 5 Chirality restraints: 1783 Sorted by residual: chirality pdb=" CA MET f 125 " pdb=" N MET f 125 " pdb=" C MET f 125 " pdb=" CB MET f 125 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA THR g 35 " pdb=" N THR g 35 " pdb=" C THR g 35 " pdb=" CB THR g 35 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA THR p 35 " pdb=" N THR p 35 " pdb=" C THR p 35 " pdb=" CB THR p 35 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1780 not shown) Planarity restraints: 2002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE g 116 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C ILE g 116 " -0.043 2.00e-02 2.50e+03 pdb=" O ILE g 116 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU g 117 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU g 117 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C GLU g 117 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU g 117 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL g 118 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS h 128 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C LYS h 128 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS h 128 " 0.010 2.00e-02 2.50e+03 pdb=" N THR h 129 " 0.010 2.00e-02 2.50e+03 ... (remaining 1999 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 92 2.57 - 3.16: 9198 3.16 - 3.74: 16917 3.74 - 4.32: 19932 4.32 - 4.90: 34973 Nonbonded interactions: 81112 Sorted by model distance: nonbonded pdb=" O UNK 2 9 " pdb=" ND2 ASN i 104 " model vdw 1.992 2.520 nonbonded pdb=" OG1 THR 9 330 " pdb=" OD1 ASP j 38 " model vdw 2.155 2.440 nonbonded pdb=" OG SER h 12 " pdb=" O VAL h 62 " model vdw 2.172 2.440 nonbonded pdb=" OH TYR o 116 " pdb=" OG1 THR p 129 " model vdw 2.289 2.440 nonbonded pdb=" OD1 ASN h 27 " pdb=" OH TYR h 42 " model vdw 2.292 2.440 ... (remaining 81107 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' } ncs_group { reference = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } ncs_group { reference = (chain 'f' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'g' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'h' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'i' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'j' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'p' and (resid 2 through 53 or resid 59 through 132)) } ncs_group { reference = (chain 'k' and (resid 3 through 54 or resid 82 through 135)) selection = chain 'l' selection = chain 'm' selection = (chain 'n' and (resid 3 through 54 or resid 82 through 135)) selection = (chain 'o' and (resid 3 through 54 or resid 82 through 135)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.190 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: 28.460 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.680 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.050 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.003 0.040 11043 Z= 0.221 Angle : 0.531 6.410 14982 Z= 0.282 Chirality : 0.038 0.148 1783 Planarity : 0.003 0.035 2002 Dihedral : 11.229 89.246 4069 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 2.56 % 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: 3.52 (0.24), residues: 1358 helix: 4.00 (0.19), residues: 723 sheet: -2.02 (0.37), residues: 137 loop : 1.18 (0.31), residues: 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 561 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 5 residues processed: 577 average time/residue: 0.2410 time to fit residues: 189.1836 Evaluate side-chains 446 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 441 time to evaluate : 1.262 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1519 time to fit residues: 2.8851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.0060 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 30 ASN f 88 ASN g 27 ASN g 104 ASN g 113 GLN h 22 ASN j 30 ASN l 12 GLN l 21 GLN l 23 GLN m 32 ASN m 112 ASN ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 30 ASN k 32 ASN k 92 GLN k 132 ASN n 112 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11043 Z= 0.207 Angle : 0.561 7.940 14982 Z= 0.279 Chirality : 0.039 0.163 1783 Planarity : 0.004 0.042 2002 Dihedral : 3.350 18.383 1555 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 4.50 % 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: 3.35 (0.24), residues: 1358 helix: 3.83 (0.19), residues: 718 sheet: -1.74 (0.38), residues: 140 loop : 1.07 (0.30), residues: 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 461 time to evaluate : 1.270 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 28 residues processed: 484 average time/residue: 0.2472 time to fit residues: 163.9399 Evaluate side-chains 471 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 443 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1023 time to fit residues: 6.9595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 324 ASN g 104 ASN g 113 GLN h 22 ASN h 30 ASN h 113 GLN j 30 ASN l 12 GLN l 108 GLN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 17 ASN n 21 GLN ** n 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.063 11043 Z= 0.458 Angle : 0.713 8.509 14982 Z= 0.361 Chirality : 0.045 0.169 1783 Planarity : 0.005 0.046 2002 Dihedral : 4.071 20.957 1555 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 4.32 % 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: 2.38 (0.23), residues: 1358 helix: 2.99 (0.18), residues: 718 sheet: -2.13 (0.38), residues: 123 loop : 0.59 (0.28), residues: 517 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 476 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 34 residues processed: 498 average time/residue: 0.2382 time to fit residues: 161.9187 Evaluate side-chains 483 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 449 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1108 time to fit residues: 8.3271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 111 optimal weight: 0.1980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 113 GLN j 113 GLN j 115 ASN l 108 GLN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 GLN ** o 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 22 ASN p 120 ASN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 117 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11043 Z= 0.181 Angle : 0.581 7.898 14982 Z= 0.284 Chirality : 0.039 0.150 1783 Planarity : 0.003 0.040 2002 Dihedral : 3.562 19.539 1555 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 2.65 % 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: 2.88 (0.23), residues: 1358 helix: 3.33 (0.19), residues: 724 sheet: -1.74 (0.39), residues: 119 loop : 0.83 (0.29), residues: 515 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 475 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 490 average time/residue: 0.2517 time to fit residues: 169.4725 Evaluate side-chains 474 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 458 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1033 time to fit residues: 4.7564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 99 optimal weight: 0.4980 chunk 55 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 0.0670 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 0.0470 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 22 ASN f 46 GLN g 113 GLN j 115 ASN l 23 GLN l 108 GLN l 112 ASN ** m 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN m 92 GLN ** m 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 GLN o 135 GLN p 22 ASN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11043 Z= 0.173 Angle : 0.575 8.930 14982 Z= 0.282 Chirality : 0.039 0.164 1783 Planarity : 0.003 0.035 2002 Dihedral : 3.454 18.479 1555 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 2.91 % 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: 2.89 (0.23), residues: 1358 helix: 3.29 (0.19), residues: 725 sheet: -1.78 (0.39), residues: 119 loop : 0.91 (0.29), residues: 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 469 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 21 residues processed: 478 average time/residue: 0.2369 time to fit residues: 156.0888 Evaluate side-chains 467 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 446 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1150 time to fit residues: 5.8260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 46 GLN g 113 GLN j 115 ASN m 32 ASN m 112 ASN ** m 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 115 ASN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11043 Z= 0.179 Angle : 0.603 14.482 14982 Z= 0.288 Chirality : 0.038 0.167 1783 Planarity : 0.003 0.035 2002 Dihedral : 3.402 18.519 1555 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 2.47 % 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: 2.99 (0.24), residues: 1358 helix: 3.37 (0.19), residues: 725 sheet: -1.76 (0.40), residues: 119 loop : 0.97 (0.29), residues: 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 456 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 467 average time/residue: 0.2395 time to fit residues: 153.2342 Evaluate side-chains 460 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 445 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1173 time to fit residues: 4.7727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 46 GLN g 113 GLN j 115 ASN l 108 GLN m 32 ASN o 112 ASN o 126 GLN p 22 ASN k 132 ASN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11043 Z= 0.214 Angle : 0.604 11.374 14982 Z= 0.294 Chirality : 0.039 0.173 1783 Planarity : 0.003 0.035 2002 Dihedral : 3.465 18.648 1555 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 2.82 % 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: 2.93 (0.23), residues: 1358 helix: 3.32 (0.19), residues: 726 sheet: -1.82 (0.39), residues: 119 loop : 0.97 (0.29), residues: 513 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 466 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 477 average time/residue: 0.2338 time to fit residues: 155.3103 Evaluate side-chains 465 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 448 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0992 time to fit residues: 4.7815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 104 optimal weight: 0.0670 chunk 120 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 46 GLN g 113 GLN j 115 ASN l 12 GLN m 132 ASN o 112 ASN p 22 ASN k 132 ASN n 23 GLN ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11043 Z= 0.176 Angle : 0.625 12.245 14982 Z= 0.299 Chirality : 0.039 0.171 1783 Planarity : 0.003 0.033 2002 Dihedral : 3.406 17.876 1555 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.32 % 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: 3.05 (0.24), residues: 1358 helix: 3.40 (0.19), residues: 725 sheet: -1.97 (0.40), residues: 121 loop : 1.12 (0.29), residues: 512 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 463 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 468 average time/residue: 0.2425 time to fit residues: 155.6057 Evaluate side-chains 454 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 446 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0978 time to fit residues: 3.1742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 0.0570 chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 0.0970 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 0.0470 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 46 GLN f 113 GLN g 113 GLN g 115 ASN j 115 ASN ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 22 ASN k 132 ASN ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11043 Z= 0.168 Angle : 0.630 11.176 14982 Z= 0.299 Chirality : 0.039 0.165 1783 Planarity : 0.003 0.031 2002 Dihedral : 3.321 16.929 1555 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 0.88 % 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: 3.09 (0.24), residues: 1358 helix: 3.41 (0.19), residues: 726 sheet: -1.76 (0.40), residues: 124 loop : 1.13 (0.30), residues: 508 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 458 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 459 average time/residue: 0.2510 time to fit residues: 158.0236 Evaluate side-chains 449 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 445 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1241 time to fit residues: 2.5402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 46 GLN g 104 ASN g 113 GLN g 115 ASN h 46 GLN j 115 ASN ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 22 ASN k 132 ASN ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11043 Z= 0.263 Angle : 0.681 11.331 14982 Z= 0.325 Chirality : 0.041 0.161 1783 Planarity : 0.004 0.034 2002 Dihedral : 3.499 18.350 1555 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.53 % 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: 2.87 (0.24), residues: 1358 helix: 3.23 (0.19), residues: 728 sheet: -1.79 (0.40), residues: 134 loop : 1.08 (0.30), residues: 496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 453 time to evaluate : 1.276 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 456 average time/residue: 0.2525 time to fit residues: 156.6203 Evaluate side-chains 452 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 449 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1009 time to fit residues: 2.3315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 46 GLN g 113 GLN g 115 ASN j 115 ASN p 22 ASN p 40 GLN k 132 ASN ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.127902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.109436 restraints weight = 18025.469| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.53 r_work: 0.3406 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11043 Z= 0.197 Angle : 0.660 11.538 14982 Z= 0.313 Chirality : 0.039 0.165 1783 Planarity : 0.003 0.038 2002 Dihedral : 3.446 18.266 1555 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.62 % 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: 2.95 (0.24), residues: 1358 helix: 3.27 (0.19), residues: 728 sheet: -1.74 (0.40), residues: 129 loop : 1.11 (0.30), residues: 501 =============================================================================== Job complete usr+sys time: 3496.83 seconds wall clock time: 63 minutes 24.14 seconds (3804.14 seconds total)