Starting phenix.real_space_refine on Wed Nov 15 05:27:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5a_33013/11_2023/7x5a_33013.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5a_33013/11_2023/7x5a_33013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5a_33013/11_2023/7x5a_33013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5a_33013/11_2023/7x5a_33013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5a_33013/11_2023/7x5a_33013.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5a_33013/11_2023/7x5a_33013.pdb" } resolution = 3.01 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= 0.078 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 104 5.49 5 S 32 5.16 5 C 6510 2.51 5 N 1888 2.21 5 O 2152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 96": "OD1" <-> "OD2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G GLU 65": "OE1" <-> "OE2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G ASP 130": "OD1" <-> "OD2" Residue "H ASP 20": "OD1" <-> "OD2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H ASP 106": "OD1" <-> "OD2" Residue "H GLU 127": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 10686 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 535 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 532 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "K" Number of atoms: 533 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 533 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "L" Number of atoms: 532 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 532 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1083 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 129} Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "C" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "D" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 128} Chain: "E" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "F" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "G" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "H" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P A DT I 36 " occ=0.25 ... (18 atoms not shown) pdb=" C6 A DT I 36 " occ=0.25 residue: pdb=" P A DA I 42 " occ=0.25 ... (19 atoms not shown) pdb=" C4 A DA I 42 " occ=0.25 residue: pdb=" P A DA K 20 " occ=0.25 ... (19 atoms not shown) pdb=" C4 A DA K 20 " occ=0.25 residue: pdb=" P A DT K 26 " occ=0.25 ... (18 atoms not shown) pdb=" C6 A DT K 26 " occ=0.25 Time building chain proxies: 5.80, per 1000 atoms: 0.54 Number of scatterers: 10686 At special positions: 0 Unit cell: (98.77, 112.88, 121.18, 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 32 16.00 P 104 15.00 O 2152 8.00 N 1888 7.00 C 6510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 47.6% alpha, 11.8% beta 36 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 106 through 113 removed outlier: 4.209A pdb=" N LEU A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'B' and resid 31 through 37 removed outlier: 3.570A pdb=" N ARG B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 106 through 113 removed outlier: 4.032A pdb=" N LEU C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 65 through 78 removed outlier: 3.605A pdb=" N LEU D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.607A pdb=" N LYS D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 132 removed outlier: 4.088A pdb=" N ASP D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 82 through 93 Processing helix chain 'E' and resid 94 through 105 Processing helix chain 'E' and resid 106 through 113 removed outlier: 3.868A pdb=" N LEU E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 132 removed outlier: 4.122A pdb=" N ASP E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 36 Processing helix chain 'F' and resid 65 through 77 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 94 through 105 Processing helix chain 'F' and resid 107 through 113 removed outlier: 3.871A pdb=" N ILE F 113 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 128 removed outlier: 3.562A pdb=" N ALA F 121 " --> pdb=" O GLY F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 37 removed outlier: 3.701A pdb=" N ARG G 37 " --> pdb=" O THR G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 94 through 105 Processing helix chain 'G' and resid 106 through 113 removed outlier: 4.124A pdb=" N LEU G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE G 113 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'H' and resid 31 through 36 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.501A pdb=" N LYS H 112 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 132 removed outlier: 3.871A pdb=" N ASP H 130 " --> pdb=" O VAL H 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 13 removed outlier: 6.766A pdb=" N ILE A 18 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS A 12 " --> pdb=" O HIS A 16 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N HIS A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 24 through 29 current: chain 'A' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 61 current: chain 'B' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 24 through 29 current: chain 'B' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 61 current: chain 'C' and resid 16 through 21 removed outlier: 3.507A pdb=" N VAL C 24 " --> pdb=" O VAL C 21 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 24 through 29 current: chain 'C' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 61 current: chain 'D' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 24 through 29 current: chain 'D' and resid 58 through 61 Processing sheet with id=AA2, first strand: chain 'E' and resid 2 through 13 removed outlier: 3.628A pdb=" N THR E 8 " --> pdb=" O ASP E 20 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE E 18 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS E 12 " --> pdb=" O HIS E 16 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N HIS E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 24 through 29 current: chain 'E' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 58 through 61 current: chain 'F' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 24 through 29 current: chain 'F' and resid 57 through 61 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 57 through 61 current: chain 'G' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 24 through 29 current: chain 'G' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 58 through 61 current: chain 'H' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 24 through 29 current: chain 'H' and resid 57 through 61 356 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 5.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2914 1.34 - 1.45: 2025 1.45 - 1.57: 5887 1.57 - 1.69: 204 1.69 - 1.81: 56 Bond restraints: 11086 Sorted by residual: bond pdb=" N9 DA K 11 " pdb=" C1'A DA K 11 " ideal model delta sigma weight residual 1.460 1.502 -0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" N9 DA K 13 " pdb=" C1'A DA K 13 " ideal model delta sigma weight residual 1.460 1.502 -0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" N9 DA K 27 " pdb=" C1'A DA K 27 " ideal model delta sigma weight residual 1.460 1.501 -0.041 2.00e-02 2.50e+03 4.27e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 ... (remaining 11081 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.51: 917 106.51 - 113.38: 6122 113.38 - 120.26: 4011 120.26 - 127.13: 4070 127.13 - 134.00: 319 Bond angle restraints: 15439 Sorted by residual: angle pdb=" C3'A DA K 13 " pdb=" C2'A DA K 13 " pdb=" C1'A DA K 13 " ideal model delta sigma weight residual 101.60 105.61 -4.01 1.50e+00 4.44e-01 7.15e+00 angle pdb=" C3'A DA J 25 " pdb=" C2'A DA J 25 " pdb=" C1'A DA J 25 " ideal model delta sigma weight residual 101.60 105.55 -3.95 1.50e+00 4.44e-01 6.93e+00 angle pdb=" C4'A DA K 13 " pdb=" C3'A DA K 13 " pdb=" O3'A DA K 13 " ideal model delta sigma weight residual 110.00 113.65 -3.65 1.50e+00 4.44e-01 5.91e+00 angle pdb=" C3'A DA J 32 " pdb=" C2'A DA J 32 " pdb=" C1'A DA J 32 " ideal model delta sigma weight residual 101.60 105.13 -3.53 1.50e+00 4.44e-01 5.54e+00 angle pdb=" C4 A DT K 26 " pdb=" C5 A DT K 26 " pdb=" C7 A DT K 26 " ideal model delta sigma weight residual 122.40 118.94 3.46 1.50e+00 4.44e-01 5.31e+00 ... (remaining 15434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.37: 5750 31.37 - 62.74: 594 62.74 - 94.10: 18 94.10 - 125.47: 1 125.47 - 156.84: 2 Dihedral angle restraints: 6365 sinusoidal: 3276 harmonic: 3089 Sorted by residual: dihedral pdb=" C4'A DA I 20 " pdb=" C3'A DA I 20 " pdb=" O3'A DA I 20 " pdb=" P A DA I 21 " ideal model delta sinusoidal sigma weight residual 220.00 63.16 156.84 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4'A DT L 44 " pdb=" C3'A DT L 44 " pdb=" O3'A DT L 44 " pdb=" P A DT L 45 " ideal model delta sinusoidal sigma weight residual 220.00 65.27 154.73 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA LYS F 129 " pdb=" C LYS F 129 " pdb=" N ASP F 130 " pdb=" CA ASP F 130 " ideal model delta harmonic sigma weight residual -180.00 -162.89 -17.11 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 6362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1156 0.028 - 0.056: 404 0.056 - 0.083: 116 0.083 - 0.111: 84 0.111 - 0.139: 43 Chirality restraints: 1803 Sorted by residual: chirality pdb=" CA ILE B 113 " pdb=" N ILE B 113 " pdb=" C ILE B 113 " pdb=" CB ILE B 113 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE D 113 " pdb=" N ILE D 113 " pdb=" C ILE D 113 " pdb=" CB ILE D 113 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE E 113 " pdb=" N ILE E 113 " pdb=" C ILE E 113 " pdb=" CB ILE E 113 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1800 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 38 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO D 39 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 39 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 39 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 113 " 0.021 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO F 114 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 114 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 114 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 118 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C LYS C 118 " -0.020 2.00e-02 2.50e+03 pdb=" O LYS C 118 " 0.008 2.00e-02 2.50e+03 pdb=" N LYS C 119 " 0.007 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 547 2.73 - 3.27: 9924 3.27 - 3.81: 18441 3.81 - 4.36: 22135 4.36 - 4.90: 36510 Nonbonded interactions: 87557 Sorted by model distance: nonbonded pdb=" O LYS H 118 " pdb=" OE1 GLU H 122 " model vdw 2.182 3.040 nonbonded pdb=" O VAL C 126 " pdb=" NZ LYS G 119 " model vdw 2.183 2.520 nonbonded pdb=" OP1A DA K 30 " pdb=" OG1 THR A 120 " model vdw 2.206 2.440 nonbonded pdb=" O ARG E 123 " pdb=" OE1 GLU E 127 " model vdw 2.241 3.040 nonbonded pdb=" O LYS H 118 " pdb=" N ALA H 121 " model vdw 2.248 2.520 ... (remaining 87552 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 1 through 135) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 1 through 135) selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'K' and (resid 12 through 22 or resid 24 through 30 or resid 32 through 3 \ 6)) selection = (chain 'L' and (resid 21 through 24 or resid 26 through 32 or resid 34 through 4 \ 5)) } 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=0.25 max=1.00 mean=0.92 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.320 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: 23.120 Check model and map are aligned: 0.190 Set scattering table: 0.090 Process input model: 34.520 Find NCS groups from input model: 0.680 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11086 Z= 0.163 Angle : 0.534 4.193 15439 Z= 0.310 Chirality : 0.040 0.139 1803 Planarity : 0.003 0.052 1598 Dihedral : 20.345 156.839 4375 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 1067 helix: 1.12 (0.25), residues: 507 sheet: -1.52 (0.30), residues: 268 loop : 0.45 (0.42), residues: 292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.295 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3283 time to fit residues: 93.8848 Evaluate side-chains 174 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.0670 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11086 Z= 0.173 Angle : 0.524 6.491 15439 Z= 0.291 Chirality : 0.038 0.140 1803 Planarity : 0.004 0.032 1598 Dihedral : 23.938 152.606 2215 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.97 % Allowed : 6.98 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.28), residues: 1067 helix: 1.06 (0.24), residues: 513 sheet: -1.33 (0.28), residues: 324 loop : 1.07 (0.51), residues: 230 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 1.053 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 191 average time/residue: 0.3613 time to fit residues: 87.7434 Evaluate side-chains 173 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1072 time to fit residues: 2.0458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11086 Z= 0.420 Angle : 0.637 7.401 15439 Z= 0.331 Chirality : 0.042 0.146 1803 Planarity : 0.005 0.041 1598 Dihedral : 24.326 153.974 2215 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.72 % Allowed : 8.16 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 1067 helix: 0.95 (0.24), residues: 490 sheet: -1.34 (0.28), residues: 278 loop : 0.56 (0.42), residues: 299 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 1.120 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 186 average time/residue: 0.3631 time to fit residues: 84.7277 Evaluate side-chains 182 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2262 time to fit residues: 3.9500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 48 optimal weight: 0.0050 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 0.0070 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11086 Z= 0.158 Angle : 0.516 6.049 15439 Z= 0.284 Chirality : 0.037 0.132 1803 Planarity : 0.004 0.033 1598 Dihedral : 24.169 153.758 2215 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.18 % Allowed : 9.56 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.27), residues: 1067 helix: 1.02 (0.24), residues: 499 sheet: -1.32 (0.29), residues: 280 loop : 0.69 (0.43), residues: 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 1.186 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 179 average time/residue: 0.3610 time to fit residues: 81.4047 Evaluate side-chains 170 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1499 time to fit residues: 2.8454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11086 Z= 0.250 Angle : 0.548 6.634 15439 Z= 0.294 Chirality : 0.038 0.131 1803 Planarity : 0.004 0.032 1598 Dihedral : 24.216 154.102 2215 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.43 % Allowed : 11.28 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 1067 helix: 0.99 (0.24), residues: 497 sheet: -1.32 (0.28), residues: 278 loop : 0.65 (0.42), residues: 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 169 time to evaluate : 1.190 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 172 average time/residue: 0.3669 time to fit residues: 80.0102 Evaluate side-chains 173 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3573 time to fit residues: 2.4626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11086 Z= 0.163 Angle : 0.509 5.846 15439 Z= 0.280 Chirality : 0.037 0.132 1803 Planarity : 0.004 0.032 1598 Dihedral : 24.130 153.864 2215 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.86 % Allowed : 11.71 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 1067 helix: 1.01 (0.24), residues: 501 sheet: -1.27 (0.29), residues: 280 loop : 0.70 (0.43), residues: 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 178 time to evaluate : 1.187 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 179 average time/residue: 0.3558 time to fit residues: 80.8260 Evaluate side-chains 175 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1014 time to fit residues: 2.2188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.0030 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11086 Z= 0.187 Angle : 0.521 6.098 15439 Z= 0.285 Chirality : 0.037 0.132 1803 Planarity : 0.004 0.031 1598 Dihedral : 24.120 153.944 2215 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.75 % Allowed : 12.14 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.27), residues: 1067 helix: 1.03 (0.24), residues: 499 sheet: -1.27 (0.29), residues: 278 loop : 0.70 (0.42), residues: 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 171 time to evaluate : 1.186 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 175 average time/residue: 0.3630 time to fit residues: 81.4682 Evaluate side-chains 178 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3301 time to fit residues: 3.1979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11086 Z= 0.200 Angle : 0.525 6.124 15439 Z= 0.286 Chirality : 0.037 0.132 1803 Planarity : 0.004 0.031 1598 Dihedral : 24.115 153.926 2215 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.54 % Allowed : 12.78 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 1067 helix: 1.05 (0.24), residues: 497 sheet: -1.25 (0.29), residues: 280 loop : 0.76 (0.42), residues: 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 1.183 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 181 average time/residue: 0.3602 time to fit residues: 82.7900 Evaluate side-chains 171 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11086 Z= 0.210 Angle : 0.532 6.131 15439 Z= 0.289 Chirality : 0.038 0.155 1803 Planarity : 0.004 0.031 1598 Dihedral : 24.111 153.995 2215 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.64 % Allowed : 13.00 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.27), residues: 1067 helix: 1.04 (0.24), residues: 497 sheet: -1.25 (0.29), residues: 280 loop : 0.75 (0.43), residues: 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 1.126 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 172 average time/residue: 0.3666 time to fit residues: 80.0334 Evaluate side-chains 172 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3317 time to fit residues: 2.8555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.0170 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11086 Z= 0.173 Angle : 0.516 5.767 15439 Z= 0.284 Chirality : 0.037 0.133 1803 Planarity : 0.004 0.031 1598 Dihedral : 24.044 153.757 2215 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.11 % Allowed : 13.64 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.27), residues: 1067 helix: 1.07 (0.24), residues: 501 sheet: -1.24 (0.29), residues: 280 loop : 0.80 (0.43), residues: 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.127 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.3747 time to fit residues: 81.1355 Evaluate side-chains 167 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 24 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 0.0170 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.184209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129183 restraints weight = 11257.438| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.24 r_work: 0.3323 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11086 Z= 0.153 Angle : 0.503 5.708 15439 Z= 0.278 Chirality : 0.037 0.133 1803 Planarity : 0.004 0.030 1598 Dihedral : 23.981 153.424 2215 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.32 % Allowed : 13.75 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 1067 helix: 0.98 (0.24), residues: 513 sheet: -1.22 (0.29), residues: 280 loop : 0.73 (0.44), residues: 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2853.95 seconds wall clock time: 52 minutes 21.05 seconds (3141.05 seconds total)