Starting phenix.real_space_refine on Mon Aug 5 06:39:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txx_41708/08_2024/8txx_41708.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txx_41708/08_2024/8txx_41708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txx_41708/08_2024/8txx_41708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txx_41708/08_2024/8txx_41708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txx_41708/08_2024/8txx_41708.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txx_41708/08_2024/8txx_41708.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 15 5.16 5 C 7227 2.51 5 N 2431 2.21 5 O 3002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 77": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 68": "OD1" <-> "OD2" Residue "K TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12969 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 251 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain breaks: 1 Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 Time building chain proxies: 7.39, per 1000 atoms: 0.57 Number of scatterers: 12969 At special positions: 0 Unit cell: (99.6, 124.832, 123.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 294 15.00 O 3002 8.00 N 2431 7.00 C 7227 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: 6.27 Conformation dependent library (CDL) restraints added in 1.4 seconds 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 67.9% alpha, 3.7% beta 135 base pairs and 242 stacking pairs defined. Time for finding SS restraints: 5.62 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.724A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.169A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.090A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.647A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.668A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.581A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.687A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.538A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.121A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.506A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 447 through 461 Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 56 through 60 Processing helix chain 'M' and resid 71 through 75 removed outlier: 3.745A pdb=" N ARG M 74 " --> pdb=" O LEU M 71 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY M 75 " --> pdb=" O ARG M 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 71 through 75' Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.521A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 38 removed outlier: 3.608A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.681A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.477A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.597A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.297A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 15 Processing sheet with id=AB3, first strand: chain 'M' and resid 44 through 45 435 hydrogen bonds defined for protein. 1267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 242 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 6.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2733 1.33 - 1.45: 4234 1.45 - 1.57: 6212 1.57 - 1.69: 586 1.69 - 1.81: 26 Bond restraints: 13791 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" CG GLN A 125 " pdb=" CD GLN A 125 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.03e+00 bond pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.25e-01 bond pdb=" CD LYS B 79 " pdb=" CE LYS B 79 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.13e-01 bond pdb=" CB GLN A 76 " pdb=" CG GLN A 76 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.99e-01 ... (remaining 13786 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.24: 1273 105.24 - 112.04: 7666 112.04 - 118.85: 3400 118.85 - 125.66: 6537 125.66 - 132.46: 996 Bond angle restraints: 19872 Sorted by residual: angle pdb=" C ILE A 124 " pdb=" N GLN A 125 " pdb=" CA GLN A 125 " ideal model delta sigma weight residual 120.72 115.00 5.72 1.67e+00 3.59e-01 1.17e+01 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.23e+00 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 110.77 116.37 -5.60 1.93e+00 2.68e-01 8.43e+00 angle pdb=" N GLN A 125 " pdb=" CA GLN A 125 " pdb=" CB GLN A 125 " ideal model delta sigma weight residual 110.39 114.91 -4.52 1.66e+00 3.63e-01 7.40e+00 angle pdb=" CA GLN A 76 " pdb=" CB GLN A 76 " pdb=" CG GLN A 76 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.31e+00 ... (remaining 19867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.52: 6036 31.52 - 63.04: 1497 63.04 - 94.56: 42 94.56 - 126.09: 1 126.09 - 157.61: 2 Dihedral angle restraints: 7578 sinusoidal: 5048 harmonic: 2530 Sorted by residual: dihedral pdb=" CA TYR K 474 " pdb=" C TYR K 474 " pdb=" N HIS K 475 " pdb=" CA HIS K 475 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 62.39 157.61 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 78.91 141.09 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 7575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1640 0.031 - 0.061: 464 0.061 - 0.092: 109 0.092 - 0.123: 40 0.123 - 0.154: 8 Chirality restraints: 2261 Sorted by residual: chirality pdb=" CA ASN C 38 " pdb=" N ASN C 38 " pdb=" C ASN C 38 " pdb=" CB ASN C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA GLN A 125 " pdb=" N GLN A 125 " pdb=" C GLN A 125 " pdb=" CB GLN A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 2258 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " -0.010 2.00e-02 2.50e+03 1.17e-02 2.74e+00 pdb=" CG TYR D 83 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.022 2.00e-02 2.50e+03 8.95e-03 2.40e+00 pdb=" N9 DG I 47 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.021 2.00e-02 2.50e+03 8.94e-03 2.20e+00 pdb=" N9 DA I -35 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.000 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.002 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 3 2.04 - 2.76: 1715 2.76 - 3.47: 17649 3.47 - 4.19: 34800 4.19 - 4.90: 52968 Nonbonded interactions: 107135 Sorted by model distance: nonbonded pdb=" C SER D 123 " pdb=" N SER C 11 " model vdw 1.329 3.350 nonbonded pdb=" C SER H 123 " pdb=" N SER G 11 " model vdw 1.330 3.350 nonbonded pdb=" C GLY M 76 " pdb=" NZ LYS G 15 " model vdw 1.367 3.350 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.074 3.040 nonbonded pdb=" OH TYR D 40 " pdb=" OP1 DG J 48 " model vdw 2.102 3.040 ... (remaining 107130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 39.780 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13791 Z= 0.195 Angle : 0.551 6.929 19872 Z= 0.327 Chirality : 0.033 0.154 2261 Planarity : 0.003 0.036 1500 Dihedral : 26.694 157.607 5946 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 2.62 (0.29), residues: 853 helix: 2.67 (0.22), residues: 560 sheet: 1.12 (1.38), residues: 17 loop : -0.21 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS H 109 PHE 0.010 0.001 PHE E 104 TYR 0.028 0.002 TYR D 83 ARG 0.005 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8504 (mmm) cc_final: 0.8053 (tpp) REVERT: A 123 ASP cc_start: 0.8817 (m-30) cc_final: 0.8567 (m-30) REVERT: B 27 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8914 (mp10) REVERT: B 88 TYR cc_start: 0.8607 (m-80) cc_final: 0.8082 (m-10) REVERT: D 51 ASP cc_start: 0.8750 (p0) cc_final: 0.8199 (p0) REVERT: D 57 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8580 (mmtp) REVERT: D 86 ARG cc_start: 0.9070 (mmt-90) cc_final: 0.8801 (mtt-85) REVERT: E 59 GLU cc_start: 0.8380 (pm20) cc_final: 0.7987 (pm20) REVERT: E 76 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8467 (tm-30) REVERT: F 88 TYR cc_start: 0.8759 (m-80) cc_final: 0.8445 (m-80) REVERT: H 33 ARG cc_start: 0.8429 (mtp85) cc_final: 0.7809 (mtp-110) REVERT: H 42 TYR cc_start: 0.8941 (t80) cc_final: 0.8680 (t80) REVERT: H 79 ARG cc_start: 0.8999 (ttm110) cc_final: 0.8798 (ttm-80) REVERT: C 64 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8446 (tm-30) REVERT: C 95 LYS cc_start: 0.9398 (ttmt) cc_final: 0.9191 (ttmt) REVERT: C 110 ASN cc_start: 0.8949 (t0) cc_final: 0.8344 (p0) REVERT: G 74 LYS cc_start: 0.9412 (mttp) cc_final: 0.9152 (mmtp) REVERT: G 76 THR cc_start: 0.9096 (p) cc_final: 0.8667 (t) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3086 time to fit residues: 89.5201 Evaluate side-chains 161 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 0.0000 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13791 Z= 0.268 Angle : 0.572 5.996 19872 Z= 0.339 Chirality : 0.035 0.155 2261 Planarity : 0.004 0.039 1500 Dihedral : 29.709 158.640 4186 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.17 % Allowed : 11.82 % Favored : 86.01 % 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: 2.71 (0.30), residues: 853 helix: 2.69 (0.22), residues: 575 sheet: 1.17 (1.38), residues: 17 loop : -0.26 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS H 109 PHE 0.008 0.001 PHE E 67 TYR 0.028 0.002 TYR H 40 ARG 0.003 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8699 (mmm) cc_final: 0.8169 (tpp) REVERT: B 27 GLN cc_start: 0.9261 (mm-40) cc_final: 0.9010 (mp10) REVERT: B 85 ASP cc_start: 0.8915 (m-30) cc_final: 0.8679 (m-30) REVERT: D 47 GLN cc_start: 0.8681 (mt0) cc_final: 0.8391 (mt0) REVERT: D 51 ASP cc_start: 0.8515 (p0) cc_final: 0.8081 (p0) REVERT: D 57 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8417 (mmtp) REVERT: D 86 ARG cc_start: 0.9056 (mmt-90) cc_final: 0.8801 (mtt-85) REVERT: D 108 LYS cc_start: 0.9403 (ttpt) cc_final: 0.9187 (ttpt) REVERT: E 59 GLU cc_start: 0.8416 (pm20) cc_final: 0.7976 (pm20) REVERT: F 24 ASP cc_start: 0.8168 (t0) cc_final: 0.7886 (t0) REVERT: F 88 TYR cc_start: 0.8714 (m-80) cc_final: 0.8383 (m-80) REVERT: H 33 ARG cc_start: 0.8693 (mtp85) cc_final: 0.7992 (mtp-110) REVERT: C 56 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 110 ASN cc_start: 0.9010 (t0) cc_final: 0.8382 (p0) REVERT: G 76 THR cc_start: 0.9109 (p) cc_final: 0.8620 (t) outliers start: 16 outliers final: 12 residues processed: 190 average time/residue: 0.2803 time to fit residues: 73.5029 Evaluate side-chains 182 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 95 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13791 Z= 0.341 Angle : 0.610 7.491 19872 Z= 0.358 Chirality : 0.037 0.153 2261 Planarity : 0.004 0.048 1500 Dihedral : 29.955 160.039 4186 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.53 % Allowed : 13.32 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.29), residues: 853 helix: 2.59 (0.21), residues: 576 sheet: 1.08 (1.35), residues: 17 loop : -0.46 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.006 0.001 PHE C 25 TYR 0.019 0.002 TYR H 40 ARG 0.004 0.000 ARG D 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9030 (mt) cc_final: 0.8753 (mt) REVERT: A 73 GLU cc_start: 0.8185 (tt0) cc_final: 0.7829 (tt0) REVERT: A 90 MET cc_start: 0.8862 (mmm) cc_final: 0.8470 (tpp) REVERT: B 43 VAL cc_start: 0.9654 (t) cc_final: 0.9410 (p) REVERT: B 85 ASP cc_start: 0.8884 (m-30) cc_final: 0.8617 (m-30) REVERT: D 47 GLN cc_start: 0.8640 (mt0) cc_final: 0.8324 (mt0) REVERT: D 51 ASP cc_start: 0.8569 (p0) cc_final: 0.7982 (p0) REVERT: D 57 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8549 (mmtp) REVERT: D 83 TYR cc_start: 0.7754 (t80) cc_final: 0.7473 (t80) REVERT: D 86 ARG cc_start: 0.9088 (mmt-90) cc_final: 0.8818 (mtt-85) REVERT: D 105 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8385 (mm-30) REVERT: E 59 GLU cc_start: 0.8575 (pm20) cc_final: 0.8148 (pm20) REVERT: E 105 GLU cc_start: 0.8154 (tt0) cc_final: 0.7901 (tt0) REVERT: F 35 ARG cc_start: 0.8946 (mtp85) cc_final: 0.8557 (mtp85) REVERT: F 88 TYR cc_start: 0.8743 (m-80) cc_final: 0.8086 (m-80) REVERT: H 33 ARG cc_start: 0.8733 (mtp85) cc_final: 0.8004 (mtp-110) REVERT: H 120 LYS cc_start: 0.9117 (tptm) cc_final: 0.8506 (ttpp) REVERT: C 56 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8414 (tm-30) REVERT: C 110 ASN cc_start: 0.8976 (t0) cc_final: 0.8337 (p0) REVERT: G 76 THR cc_start: 0.9187 (p) cc_final: 0.8778 (t) REVERT: G 91 GLU cc_start: 0.8421 (tp30) cc_final: 0.8137 (tp30) outliers start: 26 outliers final: 21 residues processed: 186 average time/residue: 0.2859 time to fit residues: 73.3380 Evaluate side-chains 181 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13791 Z= 0.182 Angle : 0.538 6.455 19872 Z= 0.322 Chirality : 0.033 0.148 2261 Planarity : 0.003 0.037 1500 Dihedral : 29.688 159.750 4186 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.17 % Allowed : 16.85 % Favored : 80.98 % 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: 2.77 (0.30), residues: 853 helix: 2.83 (0.22), residues: 574 sheet: 0.96 (1.32), residues: 17 loop : -0.44 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.016 0.001 TYR H 40 ARG 0.003 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8924 (mt) cc_final: 0.8689 (mt) REVERT: A 90 MET cc_start: 0.8737 (mmm) cc_final: 0.8251 (tpp) REVERT: B 85 ASP cc_start: 0.8847 (m-30) cc_final: 0.8510 (m-30) REVERT: D 46 LYS cc_start: 0.9148 (mmtt) cc_final: 0.8713 (mmtm) REVERT: D 47 GLN cc_start: 0.8542 (mt0) cc_final: 0.8213 (mt0) REVERT: D 51 ASP cc_start: 0.8514 (p0) cc_final: 0.8138 (p0) REVERT: D 86 ARG cc_start: 0.9002 (mmt-90) cc_final: 0.8704 (mtt-85) REVERT: D 105 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8209 (mm-30) REVERT: E 59 GLU cc_start: 0.8594 (pm20) cc_final: 0.8226 (pm20) REVERT: E 76 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8610 (tm-30) REVERT: E 105 GLU cc_start: 0.8058 (tt0) cc_final: 0.7823 (tt0) REVERT: H 33 ARG cc_start: 0.8715 (mtp85) cc_final: 0.7957 (mtp-110) REVERT: H 120 LYS cc_start: 0.9126 (tptm) cc_final: 0.8501 (ttpp) REVERT: C 56 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8248 (tm-30) REVERT: C 110 ASN cc_start: 0.9004 (t0) cc_final: 0.8404 (p0) REVERT: G 36 LYS cc_start: 0.8998 (tppt) cc_final: 0.8718 (tppt) REVERT: G 64 GLU cc_start: 0.9331 (tm-30) cc_final: 0.9013 (tm-30) REVERT: G 76 THR cc_start: 0.9140 (p) cc_final: 0.8632 (t) REVERT: G 91 GLU cc_start: 0.8248 (tp30) cc_final: 0.7759 (tp30) outliers start: 16 outliers final: 12 residues processed: 189 average time/residue: 0.2941 time to fit residues: 76.0758 Evaluate side-chains 177 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN H 84 ASN C 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 13791 Z= 0.487 Angle : 0.690 9.567 19872 Z= 0.397 Chirality : 0.040 0.166 2261 Planarity : 0.005 0.051 1500 Dihedral : 30.243 162.643 4186 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.62 % Allowed : 15.22 % Favored : 80.16 % 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: 2.20 (0.29), residues: 853 helix: 2.40 (0.21), residues: 578 sheet: 0.67 (1.28), residues: 17 loop : -0.74 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 49 PHE 0.008 0.002 PHE H 70 TYR 0.025 0.003 TYR H 83 ARG 0.005 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 0.971 Fit side-chains REVERT: A 90 MET cc_start: 0.8926 (mmm) cc_final: 0.8363 (tpp) REVERT: B 43 VAL cc_start: 0.9707 (t) cc_final: 0.9356 (p) REVERT: B 50 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9150 (tp) REVERT: B 85 ASP cc_start: 0.8895 (m-30) cc_final: 0.8571 (m-30) REVERT: D 51 ASP cc_start: 0.8570 (p0) cc_final: 0.8019 (p0) REVERT: E 59 GLU cc_start: 0.8644 (pm20) cc_final: 0.8304 (pm20) REVERT: E 105 GLU cc_start: 0.8253 (tt0) cc_final: 0.7984 (tt0) REVERT: F 35 ARG cc_start: 0.8928 (mtp85) cc_final: 0.8694 (mtp85) REVERT: H 33 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8031 (mtp-110) REVERT: H 47 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8698 (mm-40) REVERT: H 71 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8325 (tm-30) REVERT: H 120 LYS cc_start: 0.9142 (tptm) cc_final: 0.8701 (ttmm) REVERT: C 39 TYR cc_start: 0.9173 (m-80) cc_final: 0.8863 (m-80) REVERT: C 56 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8779 (tm-30) REVERT: C 110 ASN cc_start: 0.8972 (t0) cc_final: 0.8331 (p0) REVERT: G 76 THR cc_start: 0.9248 (p) cc_final: 0.8804 (t) REVERT: G 91 GLU cc_start: 0.8440 (tp30) cc_final: 0.7965 (tp30) outliers start: 34 outliers final: 24 residues processed: 183 average time/residue: 0.2767 time to fit residues: 69.5669 Evaluate side-chains 182 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 0.0870 chunk 88 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 125 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13791 Z= 0.181 Angle : 0.550 7.776 19872 Z= 0.329 Chirality : 0.033 0.149 2261 Planarity : 0.003 0.039 1500 Dihedral : 29.743 162.409 4186 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.31 % Allowed : 17.53 % Favored : 80.16 % 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: 2.63 (0.30), residues: 853 helix: 2.78 (0.22), residues: 574 sheet: 0.62 (1.27), residues: 17 loop : -0.62 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 31 PHE 0.009 0.001 PHE A 67 TYR 0.014 0.001 TYR H 40 ARG 0.003 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8737 (tpt90) cc_final: 0.8189 (tpt90) REVERT: B 25 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8669 (t0) REVERT: D 46 LYS cc_start: 0.9116 (mmtt) cc_final: 0.8757 (mmtm) REVERT: D 47 GLN cc_start: 0.8431 (mt0) cc_final: 0.8079 (mt0) REVERT: D 51 ASP cc_start: 0.8405 (p0) cc_final: 0.7865 (p0) REVERT: D 85 LYS cc_start: 0.9324 (mmmm) cc_final: 0.9081 (mttp) REVERT: D 86 ARG cc_start: 0.8964 (mmt-90) cc_final: 0.8670 (mtt-85) REVERT: E 105 GLU cc_start: 0.8056 (tt0) cc_final: 0.7770 (tt0) REVERT: H 33 ARG cc_start: 0.8738 (mtp85) cc_final: 0.7966 (mtp-110) REVERT: H 59 MET cc_start: 0.9278 (tpp) cc_final: 0.9003 (tpp) REVERT: H 120 LYS cc_start: 0.9125 (tptm) cc_final: 0.8516 (ttpp) REVERT: C 56 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8268 (tm-30) REVERT: C 110 ASN cc_start: 0.8991 (t0) cc_final: 0.8415 (p0) REVERT: G 64 GLU cc_start: 0.9366 (tm-30) cc_final: 0.9031 (tm-30) REVERT: G 91 GLU cc_start: 0.8317 (tp30) cc_final: 0.7887 (tp30) outliers start: 17 outliers final: 10 residues processed: 192 average time/residue: 0.2892 time to fit residues: 75.7741 Evaluate side-chains 184 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 173 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0000 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13791 Z= 0.399 Angle : 0.646 8.586 19872 Z= 0.375 Chirality : 0.038 0.180 2261 Planarity : 0.004 0.047 1500 Dihedral : 30.141 164.603 4186 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.26 % Allowed : 17.39 % Favored : 79.35 % 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: 2.34 (0.29), residues: 853 helix: 2.56 (0.21), residues: 576 sheet: 0.60 (1.28), residues: 17 loop : -0.78 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 82 PHE 0.007 0.001 PHE G 25 TYR 0.025 0.002 TYR H 40 ARG 0.005 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8818 (mmm) cc_final: 0.8230 (tpp) REVERT: B 43 VAL cc_start: 0.9695 (t) cc_final: 0.9489 (m) REVERT: B 85 ASP cc_start: 0.8897 (m-30) cc_final: 0.8573 (m-30) REVERT: D 46 LYS cc_start: 0.9187 (mmtt) cc_final: 0.8932 (mmtm) REVERT: D 47 GLN cc_start: 0.8557 (mt0) cc_final: 0.8169 (mt0) REVERT: D 51 ASP cc_start: 0.8509 (p0) cc_final: 0.7996 (p0) REVERT: D 57 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8446 (mmtp) REVERT: E 56 LYS cc_start: 0.9488 (ttpp) cc_final: 0.9168 (ttpp) REVERT: E 59 GLU cc_start: 0.8793 (pm20) cc_final: 0.8200 (pm20) REVERT: E 105 GLU cc_start: 0.8088 (tt0) cc_final: 0.7830 (tt0) REVERT: H 33 ARG cc_start: 0.8867 (mtp85) cc_final: 0.8043 (mtp-110) REVERT: H 40 TYR cc_start: 0.8739 (m-10) cc_final: 0.8445 (m-10) REVERT: H 120 LYS cc_start: 0.9155 (tptm) cc_final: 0.8720 (ttmm) REVERT: C 39 TYR cc_start: 0.9060 (m-80) cc_final: 0.8770 (m-80) REVERT: C 56 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8654 (tm-30) REVERT: C 64 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8542 (tm-30) REVERT: C 110 ASN cc_start: 0.8965 (t0) cc_final: 0.8352 (p0) REVERT: G 56 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8484 (tm-30) REVERT: G 91 GLU cc_start: 0.8382 (tp30) cc_final: 0.7869 (tp30) outliers start: 24 outliers final: 19 residues processed: 181 average time/residue: 0.2823 time to fit residues: 70.3953 Evaluate side-chains 183 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.3980 chunk 83 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13791 Z= 0.241 Angle : 0.576 8.086 19872 Z= 0.341 Chirality : 0.034 0.164 2261 Planarity : 0.004 0.043 1500 Dihedral : 29.952 164.765 4186 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.85 % Allowed : 17.80 % Favored : 79.35 % 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: 2.54 (0.29), residues: 853 helix: 2.74 (0.22), residues: 574 sheet: 0.50 (1.26), residues: 17 loop : -0.75 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.016 0.002 TYR H 40 ARG 0.003 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 179 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: A 90 MET cc_start: 0.8758 (mmm) cc_final: 0.8084 (tpp) REVERT: A 129 ARG cc_start: 0.8698 (tpt90) cc_final: 0.8058 (tpt90) REVERT: B 50 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8896 (tp) REVERT: B 85 ASP cc_start: 0.8867 (m-30) cc_final: 0.8532 (m-30) REVERT: D 42 TYR cc_start: 0.8207 (t80) cc_final: 0.7384 (t80) REVERT: D 46 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8819 (mmtp) REVERT: D 47 GLN cc_start: 0.8483 (mt0) cc_final: 0.8107 (mt0) REVERT: D 51 ASP cc_start: 0.8414 (p0) cc_final: 0.7861 (p0) REVERT: D 57 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8364 (mmtp) REVERT: D 86 ARG cc_start: 0.8979 (mmt-90) cc_final: 0.8688 (mtt-85) REVERT: E 59 GLU cc_start: 0.8796 (pm20) cc_final: 0.8218 (pm20) REVERT: E 105 GLU cc_start: 0.8058 (tt0) cc_final: 0.7754 (tt0) REVERT: F 98 TYR cc_start: 0.9389 (m-10) cc_final: 0.9188 (m-10) REVERT: H 33 ARG cc_start: 0.8849 (mtp85) cc_final: 0.8017 (mtp-110) REVERT: H 59 MET cc_start: 0.9376 (tpp) cc_final: 0.9096 (tpp) REVERT: H 120 LYS cc_start: 0.9151 (tptm) cc_final: 0.8524 (ttpp) REVERT: C 56 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8340 (tm-30) REVERT: C 64 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8472 (tm-30) REVERT: C 110 ASN cc_start: 0.8965 (t0) cc_final: 0.8372 (p0) REVERT: G 64 GLU cc_start: 0.9326 (tm-30) cc_final: 0.9079 (tm-30) REVERT: G 91 GLU cc_start: 0.8337 (tp30) cc_final: 0.7930 (tp30) outliers start: 21 outliers final: 16 residues processed: 191 average time/residue: 0.2780 time to fit residues: 73.5587 Evaluate side-chains 190 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 0.0570 chunk 64 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13791 Z= 0.217 Angle : 0.572 8.238 19872 Z= 0.338 Chirality : 0.034 0.163 2261 Planarity : 0.004 0.043 1500 Dihedral : 29.956 164.832 4186 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.17 % Allowed : 18.48 % Favored : 79.35 % 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: 2.57 (0.29), residues: 853 helix: 2.76 (0.22), residues: 574 sheet: 0.53 (1.27), residues: 17 loop : -0.73 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 82 PHE 0.008 0.001 PHE A 67 TYR 0.031 0.002 TYR D 40 ARG 0.004 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.6921 (pm20) REVERT: A 90 MET cc_start: 0.8782 (mmm) cc_final: 0.8112 (tpp) REVERT: A 129 ARG cc_start: 0.8670 (tpt90) cc_final: 0.8052 (tpt90) REVERT: B 25 ASN cc_start: 0.8899 (t0) cc_final: 0.8669 (t0) REVERT: B 50 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8880 (tp) REVERT: B 85 ASP cc_start: 0.8863 (m-30) cc_final: 0.8541 (m-30) REVERT: D 42 TYR cc_start: 0.8218 (t80) cc_final: 0.7398 (t80) REVERT: D 46 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8798 (mmtp) REVERT: D 47 GLN cc_start: 0.8463 (mt0) cc_final: 0.8072 (mt0) REVERT: D 51 ASP cc_start: 0.8405 (p0) cc_final: 0.7818 (p0) REVERT: D 57 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8367 (mmtp) REVERT: D 86 ARG cc_start: 0.8973 (mmt-90) cc_final: 0.8682 (mtt-85) REVERT: E 59 GLU cc_start: 0.8782 (pm20) cc_final: 0.8215 (pm20) REVERT: E 76 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8587 (tm-30) REVERT: E 105 GLU cc_start: 0.8018 (tt0) cc_final: 0.7728 (tt0) REVERT: H 33 ARG cc_start: 0.8845 (mtp85) cc_final: 0.8010 (mtp-110) REVERT: H 40 TYR cc_start: 0.8655 (m-10) cc_final: 0.8428 (m-10) REVERT: H 59 MET cc_start: 0.9340 (tpp) cc_final: 0.9006 (tpp) REVERT: H 71 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8173 (tm-30) REVERT: H 120 LYS cc_start: 0.9125 (tptm) cc_final: 0.8536 (ttpp) REVERT: C 56 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8319 (tm-30) REVERT: C 110 ASN cc_start: 0.8963 (t0) cc_final: 0.8374 (p0) REVERT: G 56 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8506 (tm-30) REVERT: G 64 GLU cc_start: 0.9320 (tm-30) cc_final: 0.9068 (tm-30) REVERT: G 91 GLU cc_start: 0.8317 (tp30) cc_final: 0.7932 (tp30) outliers start: 16 outliers final: 12 residues processed: 181 average time/residue: 0.2783 time to fit residues: 69.6952 Evaluate side-chains 184 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13791 Z= 0.304 Angle : 0.601 9.212 19872 Z= 0.352 Chirality : 0.036 0.160 2261 Planarity : 0.004 0.046 1500 Dihedral : 30.027 165.813 4186 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.17 % Allowed : 18.48 % Favored : 79.35 % 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: 2.52 (0.29), residues: 853 helix: 2.71 (0.21), residues: 576 sheet: 0.51 (1.27), residues: 17 loop : -0.73 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 82 PHE 0.007 0.001 PHE H 70 TYR 0.028 0.002 TYR D 40 ARG 0.005 0.000 ARG C 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: A 90 MET cc_start: 0.8806 (mmm) cc_final: 0.8139 (tpp) REVERT: A 129 ARG cc_start: 0.8718 (tpt90) cc_final: 0.8055 (tpt90) REVERT: B 50 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8926 (tp) REVERT: B 85 ASP cc_start: 0.8891 (m-30) cc_final: 0.8567 (m-30) REVERT: D 42 TYR cc_start: 0.8259 (t80) cc_final: 0.7439 (t80) REVERT: D 46 LYS cc_start: 0.9232 (mmtt) cc_final: 0.8798 (mmtp) REVERT: D 47 GLN cc_start: 0.8502 (mt0) cc_final: 0.8126 (mt0) REVERT: D 51 ASP cc_start: 0.8436 (p0) cc_final: 0.7852 (p0) REVERT: D 57 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8407 (mmtp) REVERT: E 59 GLU cc_start: 0.8776 (pm20) cc_final: 0.8222 (pm20) REVERT: E 76 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8619 (tm-30) REVERT: E 105 GLU cc_start: 0.8042 (tt0) cc_final: 0.7751 (tt0) REVERT: H 33 ARG cc_start: 0.8864 (mtp85) cc_final: 0.8031 (mtp-110) REVERT: H 71 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8315 (tm-30) REVERT: H 120 LYS cc_start: 0.9152 (tptm) cc_final: 0.8531 (ttpp) REVERT: C 56 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8316 (tm-30) REVERT: C 110 ASN cc_start: 0.8972 (t0) cc_final: 0.8373 (p0) REVERT: G 64 GLU cc_start: 0.9341 (tm-30) cc_final: 0.9076 (tm-30) REVERT: G 91 GLU cc_start: 0.8395 (tp30) cc_final: 0.8015 (tp30) outliers start: 16 outliers final: 13 residues processed: 176 average time/residue: 0.2873 time to fit residues: 69.5127 Evaluate side-chains 182 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 20.0000 chunk 12 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.097310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.060887 restraints weight = 49620.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.063169 restraints weight = 22019.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.064734 restraints weight = 14149.696| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13791 Z= 0.197 Angle : 0.563 9.143 19872 Z= 0.332 Chirality : 0.033 0.143 2261 Planarity : 0.003 0.040 1500 Dihedral : 29.891 166.239 4186 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.04 % Allowed : 18.75 % Favored : 79.21 % 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: 2.64 (0.30), residues: 853 helix: 2.82 (0.22), residues: 574 sheet: 0.65 (1.30), residues: 17 loop : -0.70 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.026 0.002 TYR D 40 ARG 0.004 0.000 ARG B 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.58 seconds wall clock time: 42 minutes 54.25 seconds (2574.25 seconds total)