Starting phenix.real_space_refine (version: dev) on Fri Feb 24 09:06:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2023/7zgy_14715_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2023/7zgy_14715.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2023/7zgy_14715_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2023/7zgy_14715_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2023/7zgy_14715_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2023/7zgy_14715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2023/7zgy_14715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2023/7zgy_14715_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgy_14715/02_2023/7zgy_14715_neut_trim_updated.pdb" } resolution = 2.54 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= 0.060 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 Process input model Symmetric amino acids flipped Residue "B PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21861 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 170 Unusual residues: {' CU': 3, ' FE': 1, 'JPI': 1, 'JPX': 1, 'JQ6': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 236 Unusual residues: {' CU': 3, ' FE': 1, 'JPI': 1, 'JPX': 2, 'JQ6': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 104 Unusual residues: {' CU': 3, ' FE': 1, 'JPI': 1, 'JQ6': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 11.50, per 1000 atoms: 0.53 Number of scatterers: 21861 At special positions: 0 Unit cell: (164.418, 155.42, 128.426, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 9 28.99 Fe 3 26.01 S 18 16.00 P 6 15.00 O 4392 8.00 N 3807 7.00 C 13626 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.20 Conformation dependent library (CDL) restraints added in 3.4 seconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 32 sheets defined 6.0% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 222 through 251 removed outlier: 3.570A pdb=" N GLU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 452 through 455 No H-bonds generated for 'chain 'A' and resid 452 through 455' Processing helix chain 'A' and resid 590 through 593 No H-bonds generated for 'chain 'A' and resid 590 through 593' Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 871 through 874 Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 1030 through 1032 No H-bonds generated for 'chain 'A' and resid 1030 through 1032' Processing helix chain 'B' and resid 222 through 251 removed outlier: 3.579A pdb=" N GLU B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 452 through 455 No H-bonds generated for 'chain 'B' and resid 452 through 455' Processing helix chain 'B' and resid 590 through 593 No H-bonds generated for 'chain 'B' and resid 590 through 593' Processing helix chain 'B' and resid 785 through 787 No H-bonds generated for 'chain 'B' and resid 785 through 787' Processing helix chain 'B' and resid 871 through 874 Processing helix chain 'B' and resid 921 through 923 No H-bonds generated for 'chain 'B' and resid 921 through 923' Processing helix chain 'B' and resid 1030 through 1032 No H-bonds generated for 'chain 'B' and resid 1030 through 1032' Processing helix chain 'C' and resid 222 through 251 removed outlier: 3.604A pdb=" N GLU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 452 through 455 No H-bonds generated for 'chain 'C' and resid 452 through 455' Processing helix chain 'C' and resid 590 through 593 No H-bonds generated for 'chain 'C' and resid 590 through 593' Processing helix chain 'C' and resid 785 through 787 No H-bonds generated for 'chain 'C' and resid 785 through 787' Processing helix chain 'C' and resid 871 through 874 Processing helix chain 'C' and resid 921 through 923 No H-bonds generated for 'chain 'C' and resid 921 through 923' Processing helix chain 'C' and resid 1030 through 1032 No H-bonds generated for 'chain 'C' and resid 1030 through 1032' Processing sheet with id= A, first strand: chain 'A' and resid 1033 through 1035 removed outlier: 3.720A pdb=" N TYR A1163 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE A 262 " --> pdb=" O TYR A1163 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LEU A 390 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 429 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 267 through 269 Processing sheet with id= C, first strand: chain 'A' and resid 334 through 337 Processing sheet with id= D, first strand: chain 'A' and resid 400 through 402 Processing sheet with id= E, first strand: chain 'A' and resid 487 through 490 removed outlier: 5.807A pdb=" N VAL A 562 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS A 761 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 678 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY A 759 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR A 680 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY A 757 " --> pdb=" O TYR A 680 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 682 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN A 755 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 792 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 850 " --> pdb=" O GLY A 938 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR A 978 " --> pdb=" O THR A1001 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 819 through 821 Processing sheet with id= G, first strand: chain 'A' and resid 951 through 953 Processing sheet with id= H, first strand: chain 'A' and resid 1045 through 1048 Processing sheet with id= I, first strand: chain 'A' and resid 1088 through 1091 Processing sheet with id= J, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id= K, first strand: chain 'A' and resid 724 through 729 removed outlier: 5.767A pdb=" N ARG A 726 " --> pdb=" O LYS A 752 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS A 752 " --> pdb=" O ARG A 726 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA A 728 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASN A 750 " --> pdb=" O ALA A 728 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1033 through 1035 removed outlier: 3.730A pdb=" N TYR B1163 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE B 262 " --> pdb=" O TYR B1163 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU B 390 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 429 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 267 through 269 Processing sheet with id= N, first strand: chain 'B' and resid 334 through 337 Processing sheet with id= O, first strand: chain 'B' and resid 400 through 402 Processing sheet with id= P, first strand: chain 'B' and resid 487 through 490 removed outlier: 5.807A pdb=" N VAL B 562 " --> pdb=" O ARG B 549 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 678 " --> pdb=" O VAL B 648 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS B 761 " --> pdb=" O TYR B 676 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 678 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY B 759 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR B 680 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 757 " --> pdb=" O TYR B 680 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 682 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN B 755 " --> pdb=" O LYS B 682 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 792 " --> pdb=" O THR B 811 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 850 " --> pdb=" O GLY B 938 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR B 978 " --> pdb=" O THR B1001 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 819 through 821 Processing sheet with id= R, first strand: chain 'B' and resid 951 through 953 Processing sheet with id= S, first strand: chain 'B' and resid 1045 through 1048 Processing sheet with id= T, first strand: chain 'B' and resid 1088 through 1091 Processing sheet with id= U, first strand: chain 'B' and resid 1109 through 1111 Processing sheet with id= V, first strand: chain 'B' and resid 724 through 729 removed outlier: 5.747A pdb=" N ARG B 726 " --> pdb=" O LYS B 752 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS B 752 " --> pdb=" O ARG B 726 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA B 728 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASN B 750 " --> pdb=" O ALA B 728 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 951 through 953 removed outlier: 3.713A pdb=" N TYR C1163 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE C 262 " --> pdb=" O TYR C1163 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU C 390 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 429 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 267 through 269 Processing sheet with id= Y, first strand: chain 'C' and resid 334 through 337 Processing sheet with id= Z, first strand: chain 'C' and resid 400 through 402 Processing sheet with id= AA, first strand: chain 'C' and resid 487 through 490 removed outlier: 5.763A pdb=" N VAL C 562 " --> pdb=" O ARG C 549 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER C 622 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS C 761 " --> pdb=" O TYR C 676 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 678 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY C 759 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR C 680 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY C 757 " --> pdb=" O TYR C 680 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C 682 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN C 755 " --> pdb=" O LYS C 682 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 792 " --> pdb=" O THR C 811 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 850 " --> pdb=" O GLY C 938 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 819 through 821 Processing sheet with id= AC, first strand: chain 'C' and resid 1045 through 1048 Processing sheet with id= AD, first strand: chain 'C' and resid 1088 through 1091 Processing sheet with id= AE, first strand: chain 'C' and resid 1109 through 1111 Processing sheet with id= AF, first strand: chain 'C' and resid 724 through 729 removed outlier: 3.823A pdb=" N GLY C 754 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ARG C 726 " --> pdb=" O LYS C 752 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LYS C 752 " --> pdb=" O ARG C 726 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ALA C 728 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASN C 750 " --> pdb=" O ALA C 728 " (cutoff:3.500A) 828 hydrogen bonds defined for protein. 2274 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: 9.54 Time building geometry restraints manager: 8.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3705 1.31 - 1.44: 6378 1.44 - 1.56: 12147 1.56 - 1.68: 12 1.68 - 1.81: 30 Bond restraints: 22272 Sorted by residual: bond pdb=" C25 JPI C1201 " pdb=" C39 JPI C1201 " ideal model delta sigma weight residual 0.000 1.523 -1.523 2.00e-02 2.50e+03 5.80e+03 bond pdb=" C25 JPI B1302 " pdb=" C39 JPI B1302 " ideal model delta sigma weight residual 0.000 1.522 -1.522 2.00e-02 2.50e+03 5.79e+03 bond pdb=" C25 JPI A1201 " pdb=" C39 JPI A1201 " ideal model delta sigma weight residual 0.000 1.520 -1.520 2.00e-02 2.50e+03 5.78e+03 bond pdb=" C29 JPI B1302 " pdb=" C30 JPI B1302 " ideal model delta sigma weight residual 0.336 1.537 -1.201 2.00e-02 2.50e+03 3.61e+03 bond pdb=" C29 JPI A1201 " pdb=" C30 JPI A1201 " ideal model delta sigma weight residual 0.336 1.536 -1.200 2.00e-02 2.50e+03 3.60e+03 ... (remaining 22267 not shown) Histogram of bond angle deviations from ideal: 95.79 - 103.42: 161 103.42 - 111.05: 7991 111.05 - 118.68: 8908 118.68 - 126.31: 13048 126.31 - 133.94: 114 Bond angle restraints: 30222 Sorted by residual: angle pdb=" C6 JPI A1201 " pdb=" C5 JPI A1201 " pdb=" C7 JPI A1201 " ideal model delta sigma weight residual 107.70 126.14 -18.44 3.00e+00 1.11e-01 3.78e+01 angle pdb=" C6 JPI C1201 " pdb=" C5 JPI C1201 " pdb=" C7 JPI C1201 " ideal model delta sigma weight residual 107.70 126.06 -18.36 3.00e+00 1.11e-01 3.74e+01 angle pdb=" C ASN A 632 " pdb=" CA ASN A 632 " pdb=" CB ASN A 632 " ideal model delta sigma weight residual 116.54 109.61 6.93 1.15e+00 7.56e-01 3.63e+01 angle pdb=" C6 JPI B1302 " pdb=" C5 JPI B1302 " pdb=" C7 JPI B1302 " ideal model delta sigma weight residual 107.70 125.15 -17.45 3.00e+00 1.11e-01 3.38e+01 angle pdb=" C THR B 597 " pdb=" CA THR B 597 " pdb=" CB THR B 597 " ideal model delta sigma weight residual 116.63 110.16 6.47 1.16e+00 7.43e-01 3.11e+01 ... (remaining 30217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 12471 34.15 - 68.31: 241 68.31 - 102.46: 31 102.46 - 136.62: 4 136.62 - 170.77: 3 Dihedral angle restraints: 12750 sinusoidal: 4803 harmonic: 7947 Sorted by residual: dihedral pdb=" CA TYR C 696 " pdb=" C TYR C 696 " pdb=" N GLY C 697 " pdb=" CA GLY C 697 " ideal model delta harmonic sigma weight residual 180.00 149.79 30.21 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA TYR A 696 " pdb=" C TYR A 696 " pdb=" N GLY A 697 " pdb=" CA GLY A 697 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA TYR B 696 " pdb=" C TYR B 696 " pdb=" N GLY B 697 " pdb=" CA GLY B 697 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 12747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.050: 3252 1.050 - 2.101: 3 2.101 - 3.151: 9 3.151 - 4.201: 0 4.201 - 5.252: 6 Chirality restraints: 3270 Sorted by residual: chirality pdb=" C21 JPI C1201 " pdb=" C20 JPI C1201 " pdb=" C22 JPI C1201 " pdb=" C38 JPI C1201 " both_signs ideal model delta sigma weight residual False 2.71 -2.54 5.25 2.00e-01 2.50e+01 6.89e+02 chirality pdb=" C21 JPI B1302 " pdb=" C20 JPI B1302 " pdb=" C22 JPI B1302 " pdb=" C38 JPI B1302 " both_signs ideal model delta sigma weight residual False 2.71 -2.53 5.24 2.00e-01 2.50e+01 6.87e+02 chirality pdb=" C21 JPI A1201 " pdb=" C20 JPI A1201 " pdb=" C22 JPI A1201 " pdb=" C38 JPI A1201 " both_signs ideal model delta sigma weight residual False 2.71 -2.53 5.24 2.00e-01 2.50e+01 6.85e+02 ... (remaining 3267 not shown) Planarity restraints: 4041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 JPX B1301 " 0.119 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C3 JPX B1301 " -0.080 2.00e-02 2.50e+03 pdb=" C9 JPX B1301 " 0.349 2.00e-02 2.50e+03 pdb=" N1 JPX B1301 " -0.535 2.00e-02 2.50e+03 pdb=" O7 JPX B1301 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 JPX A1203 " -0.124 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C3 JPX A1203 " 0.073 2.00e-02 2.50e+03 pdb=" C9 JPX A1203 " -0.341 2.00e-02 2.50e+03 pdb=" N1 JPX A1203 " 0.526 2.00e-02 2.50e+03 pdb=" O7 JPX A1203 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 JQ6 C1202 " -0.069 2.00e-02 2.50e+03 2.93e-01 1.08e+03 pdb=" C16 JQ6 C1202 " 0.102 2.00e-02 2.50e+03 pdb=" C8 JQ6 C1202 " 0.338 2.00e-02 2.50e+03 pdb=" N2 JQ6 C1202 " -0.526 2.00e-02 2.50e+03 pdb=" O11 JQ6 C1202 " 0.154 2.00e-02 2.50e+03 ... (remaining 4038 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 71 2.26 - 2.92: 10321 2.92 - 3.58: 29626 3.58 - 4.24: 53958 4.24 - 4.90: 93649 Nonbonded interactions: 187625 Sorted by model distance: nonbonded pdb=" OD1 ASP C 513 " pdb="CU CU C1204 " model vdw 1.605 2.240 nonbonded pdb=" OD1 ASP B 513 " pdb="CU CU B1306 " model vdw 1.661 2.240 nonbonded pdb=" O GLY A 559 " pdb="CU CU A1204 " model vdw 1.780 2.240 nonbonded pdb=" OD1 ASN C 442 " pdb="FE FE C1206 " model vdw 1.786 2.260 nonbonded pdb=" OD1 ASP A 513 " pdb="CU CU A1205 " model vdw 1.793 2.240 ... (remaining 187620 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 218 through 1167 or resid 1205)) selection = (chain 'B' and (resid 218 through 1167 or resid 1305)) selection = (chain 'C' and (resid 218 through 1167 or resid 1205)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 3 7.16 5 Cu 9 5.60 5 P 6 5.49 5 S 18 5.16 5 C 13626 2.51 5 N 3807 2.21 5 O 4392 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 8.510 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: 0.020 Extract box with map and model: 32.810 Check model and map are aligned: 0.310 Process input model: 57.830 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.180 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.025 1.523 22272 Z= 1.725 Angle : 0.904 18.444 30222 Z= 0.415 Chirality : 0.272 5.252 3270 Planarity : 0.015 0.300 4041 Dihedral : 14.440 170.771 7818 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.24 % Favored : 89.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.16), residues: 2841 helix: -0.01 (0.41), residues: 186 sheet: -0.50 (0.16), residues: 1149 loop : -2.06 (0.15), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.458 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 1.3217 time to fit residues: 293.8515 Evaluate side-chains 107 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.645 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 134 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1052 ASN A1166 ASN B 424 ASN B1005 GLN ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1166 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.137 22272 Z= 0.401 Angle : 0.933 25.811 30222 Z= 0.419 Chirality : 0.057 0.659 3270 Planarity : 0.004 0.054 4041 Dihedral : 12.682 172.982 3393 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.28 % Favored : 89.55 % Rotamer Outliers : 1.52 % 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: -1.82 (0.16), residues: 2841 helix: -0.20 (0.40), residues: 186 sheet: -0.39 (0.16), residues: 1143 loop : -2.05 (0.15), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 2.425 Fit side-chains outliers start: 33 outliers final: 10 residues processed: 140 average time/residue: 1.1532 time to fit residues: 190.9135 Evaluate side-chains 120 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 2.366 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1878 time to fit residues: 4.1050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 256 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.137 22272 Z= 0.401 Angle : 0.933 25.811 30222 Z= 0.419 Chirality : 0.057 0.659 3270 Planarity : 0.004 0.054 4041 Dihedral : 12.682 172.982 3393 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.28 % Favored : 89.55 % Rotamer Outliers : 0.46 % 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: -1.82 (0.16), residues: 2841 helix: -0.20 (0.40), residues: 186 sheet: -0.39 (0.16), residues: 1143 loop : -2.05 (0.15), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 2.247 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 120 average time/residue: 1.2065 time to fit residues: 170.3456 Evaluate side-chains 112 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 2.393 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 3.1881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 0.8980 chunk 192 optimal weight: 0.0050 chunk 133 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 257 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.137 22272 Z= 0.401 Angle : 0.933 25.811 30222 Z= 0.419 Chirality : 0.057 0.659 3270 Planarity : 0.004 0.054 4041 Dihedral : 12.682 172.982 3393 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.28 % Favored : 89.55 % Rotamer Outliers : 0.41 % 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: -1.82 (0.16), residues: 2841 helix: -0.20 (0.40), residues: 186 sheet: -0.39 (0.16), residues: 1143 loop : -2.05 (0.15), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 2.578 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 113 average time/residue: 1.1669 time to fit residues: 156.0569 Evaluate side-chains 111 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.9911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 68 optimal weight: 0.0770 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.135 22272 Z= 0.401 Angle : 0.933 25.801 30222 Z= 0.419 Chirality : 0.057 0.659 3270 Planarity : 0.004 0.054 4041 Dihedral : 12.682 172.975 3393 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.28 % Favored : 89.55 % Rotamer Outliers : 0.46 % 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: -1.82 (0.16), residues: 2841 helix: -0.20 (0.40), residues: 186 sheet: -0.39 (0.16), residues: 1143 loop : -2.05 (0.15), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 2.268 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 113 average time/residue: 1.1472 time to fit residues: 153.5932 Evaluate side-chains 112 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 2.484 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 3.2926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 0.9980 chunk 245 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 160 optimal weight: 0.0170 chunk 67 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 chunk 226 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.126 22272 Z= 0.396 Angle : 0.936 25.746 30222 Z= 0.419 Chirality : 0.057 0.659 3270 Planarity : 0.004 0.054 4041 Dihedral : 12.682 172.947 3393 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.28 % Favored : 89.55 % Rotamer Outliers : 0.41 % 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: -1.82 (0.16), residues: 2841 helix: -0.20 (0.40), residues: 186 sheet: -0.39 (0.16), residues: 1143 loop : -2.05 (0.15), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 2.469 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 113 average time/residue: 1.1872 time to fit residues: 160.0941 Evaluate side-chains 111 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 2.384 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 3.1618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 199 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 229 optimal weight: 0.3980 chunk 152 optimal weight: 3.9990 chunk 271 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 22272 Z= 0.387 Angle : 0.935 25.627 30222 Z= 0.418 Chirality : 0.057 0.659 3270 Planarity : 0.004 0.054 4041 Dihedral : 12.681 172.881 3393 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.28 % Favored : 89.55 % Rotamer Outliers : 0.60 % 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: -1.82 (0.16), residues: 2841 helix: -0.20 (0.40), residues: 186 sheet: -0.39 (0.16), residues: 1143 loop : -2.05 (0.15), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 2.449 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 116 average time/residue: 1.2041 time to fit residues: 164.6388 Evaluate side-chains 115 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 2.356 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 3.2256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.267 22272 Z= 0.413 Angle : 0.922 24.876 30222 Z= 0.414 Chirality : 0.056 0.653 3270 Planarity : 0.004 0.054 4041 Dihedral : 12.686 172.360 3393 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.24 % Favored : 89.58 % Rotamer Outliers : 0.64 % 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: -1.82 (0.16), residues: 2841 helix: -0.21 (0.40), residues: 186 sheet: -0.39 (0.16), residues: 1143 loop : -2.04 (0.15), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 2.571 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 121 average time/residue: 1.2173 time to fit residues: 174.7695 Evaluate side-chains 113 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 2.271 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 3.1860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 0.8980 chunk 260 optimal weight: 0.7980 chunk 237 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 228 optimal weight: 0.6980 chunk 239 optimal weight: 0.2980 chunk 252 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.251 22272 Z= 0.407 Angle : 0.925 24.858 30222 Z= 0.415 Chirality : 0.056 0.654 3270 Planarity : 0.004 0.054 4041 Dihedral : 12.686 172.320 3393 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.24 % Favored : 89.58 % Rotamer Outliers : 0.46 % 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: -1.81 (0.16), residues: 2841 helix: -0.21 (0.40), residues: 186 sheet: -0.39 (0.16), residues: 1143 loop : -2.04 (0.15), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 2.286 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 115 average time/residue: 1.2160 time to fit residues: 165.9093 Evaluate side-chains 112 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 2.446 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 3.2874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 127 optimal weight: 0.0870 chunk 186 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 258 optimal weight: 0.2980 chunk 223 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.114 22272 Z= 0.247 Angle : 0.868 21.616 30222 Z= 0.399 Chirality : 0.054 0.707 3270 Planarity : 0.004 0.055 4041 Dihedral : 12.626 171.904 3393 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.21 % Favored : 89.62 % Rotamer Outliers : 0.92 % 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: -1.80 (0.16), residues: 2841 helix: -0.18 (0.40), residues: 186 sheet: -0.36 (0.16), residues: 1143 loop : -2.04 (0.15), residues: 1512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 2.448 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 1.2073 time to fit residues: 175.5414 Evaluate side-chains 116 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 1.3783 time to fit residues: 7.6458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 0.4980 chunk 238 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** C 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.112190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.089163 restraints weight = 41594.268| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.48 r_work: 0.3130 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.114 22272 Z= 0.247 Angle : 0.868 21.616 30222 Z= 0.399 Chirality : 0.054 0.707 3270 Planarity : 0.004 0.055 4041 Dihedral : 12.626 171.904 3393 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.21 % Favored : 89.62 % Rotamer Outliers : 0.46 % 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: -1.80 (0.16), residues: 2841 helix: -0.18 (0.40), residues: 186 sheet: -0.36 (0.16), residues: 1143 loop : -2.04 (0.15), residues: 1512 =============================================================================== Job complete usr+sys time: 5620.75 seconds wall clock time: 102 minutes 24.33 seconds (6144.33 seconds total)