Starting phenix.real_space_refine on Sat Dec 9 09:49:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5a_33013/12_2023/7x5a_33013.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5a_33013/12_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_33013/12_2023/7x5a_33013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5a_33013/12_2023/7x5a_33013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5a_33013/12_2023/7x5a_33013.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x5a_33013/12_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6.12, per 1000 atoms: 0.57 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: 4.73 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: 3.76 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: 2.95 Time building geometry restraints manager: 5.03 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: 5939 31.37 - 62.74: 613 62.74 - 94.10: 18 94.10 - 125.47: 1 125.47 - 156.84: 2 Dihedral angle restraints: 6573 sinusoidal: 3484 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 6570 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: 6.850 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: 22.910 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 33.610 Find NCS groups from input model: 0.700 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.040 ------------------------------------------------------------------------------- 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 : 20.334 156.839 4583 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 135 HIS 0.002 0.001 HIS B 58 PHE 0.007 0.001 PHE E 132 TYR 0.007 0.001 TYR C 36 ARG 0.003 0.000 ARG F 100 *********************** 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 : 1.191 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3285 time to fit residues: 94.2419 Evaluate side-chains 174 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3643 ------------------------------------------------------------------------------- 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: 0.1088 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= 0.171 Angle : 0.532 7.198 15439 Z= 0.294 Chirality : 0.038 0.138 1803 Planarity : 0.004 0.031 1598 Dihedral : 23.652 151.470 2423 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.18 % Allowed : 6.87 % Favored : 91.94 % 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 (0.28), residues: 1067 helix: 1.02 (0.24), residues: 513 sheet: -1.33 (0.28), residues: 324 loop : 1.07 (0.51), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 135 HIS 0.004 0.001 HIS H 58 PHE 0.010 0.002 PHE F 63 TYR 0.007 0.001 TYR F 36 ARG 0.006 0.000 ARG C 77 *********************** 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 192 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 181 time to evaluate : 1.026 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 187 average time/residue: 0.3595 time to fit residues: 85.1582 Evaluate side-chains 171 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1047 time to fit residues: 2.2218 ------------------------------------------------------------------------------- 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: 0.9980 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.0470 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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: 0.7816 moved from start: 0.1336 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= 0.209 Angle : 0.533 6.433 15439 Z= 0.290 Chirality : 0.038 0.131 1803 Planarity : 0.004 0.032 1598 Dihedral : 23.777 152.924 2423 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.50 % Allowed : 7.73 % Favored : 90.76 % 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: 0.50 (0.28), residues: 1067 helix: 1.19 (0.25), residues: 497 sheet: -1.25 (0.29), residues: 278 loop : 0.87 (0.43), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.006 0.001 HIS H 58 PHE 0.008 0.002 PHE F 63 TYR 0.010 0.001 TYR F 36 ARG 0.003 0.000 ARG B 37 *********************** 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 184 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.147 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 175 average time/residue: 0.3702 time to fit residues: 81.8627 Evaluate side-chains 166 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3213 time to fit residues: 5.1196 ------------------------------------------------------------------------------- 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: 0.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 chunk 48 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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: 0.1485 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= 0.194 Angle : 0.519 6.144 15439 Z= 0.284 Chirality : 0.038 0.131 1803 Planarity : 0.004 0.033 1598 Dihedral : 23.784 152.798 2423 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.75 % Allowed : 9.56 % Favored : 89.69 % 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: 0.44 (0.28), residues: 1067 helix: 1.14 (0.24), residues: 499 sheet: -1.26 (0.29), residues: 278 loop : 0.84 (0.43), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.005 0.001 HIS H 58 PHE 0.008 0.002 PHE F 63 TYR 0.006 0.001 TYR F 36 ARG 0.005 0.000 ARG H 67 *********************** 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 181 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 174 time to evaluate : 1.311 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 177 average time/residue: 0.4031 time to fit residues: 89.6660 Evaluate side-chains 167 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1152 time to fit residues: 1.9672 ------------------------------------------------------------------------------- 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: 0.2980 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.1602 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= 0.215 Angle : 0.531 6.824 15439 Z= 0.287 Chirality : 0.038 0.131 1803 Planarity : 0.004 0.031 1598 Dihedral : 23.795 153.073 2423 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.18 % Allowed : 9.88 % Favored : 88.94 % 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: 0.42 (0.27), residues: 1067 helix: 1.11 (0.25), residues: 497 sheet: -1.27 (0.29), residues: 278 loop : 0.82 (0.42), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.005 0.001 HIS H 58 PHE 0.008 0.002 PHE D 132 TYR 0.006 0.001 TYR F 36 ARG 0.003 0.000 ARG B 37 *********************** 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 180 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 1.010 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 173 average time/residue: 0.3684 time to fit residues: 80.8478 Evaluate side-chains 175 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2825 time to fit residues: 3.2075 ------------------------------------------------------------------------------- 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: 0.5980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.0030 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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: 0.7811 moved from start: 0.1700 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= 0.177 Angle : 0.511 5.771 15439 Z= 0.280 Chirality : 0.037 0.132 1803 Planarity : 0.003 0.030 1598 Dihedral : 23.743 152.998 2423 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.97 % Allowed : 10.74 % 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: 0.44 (0.27), residues: 1067 helix: 1.13 (0.24), residues: 499 sheet: -1.27 (0.29), residues: 278 loop : 0.84 (0.42), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.004 0.001 HIS H 58 PHE 0.008 0.002 PHE F 63 TYR 0.005 0.001 TYR F 36 ARG 0.003 0.000 ARG B 37 *********************** 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 182 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 173 time to evaluate : 1.112 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 179 average time/residue: 0.3574 time to fit residues: 80.9136 Evaluate side-chains 164 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1051 time to fit residues: 1.9431 ------------------------------------------------------------------------------- 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: 0.7980 chunk 91 optimal weight: 0.1980 chunk 60 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7810 moved from start: 0.1749 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= 0.176 Angle : 0.515 5.792 15439 Z= 0.282 Chirality : 0.037 0.132 1803 Planarity : 0.004 0.032 1598 Dihedral : 23.725 152.973 2423 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.86 % Allowed : 11.39 % Favored : 87.76 % 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: 0.43 (0.27), residues: 1067 helix: 1.12 (0.24), residues: 501 sheet: -1.25 (0.29), residues: 278 loop : 0.83 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.004 0.001 HIS H 58 PHE 0.008 0.002 PHE F 63 TYR 0.005 0.001 TYR F 36 ARG 0.007 0.000 ARG F 67 *********************** 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: 8 poor density : 170 time to evaluate : 1.126 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 174 average time/residue: 0.3662 time to fit residues: 80.4945 Evaluate side-chains 164 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 160 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3518 time to fit residues: 3.1247 ------------------------------------------------------------------------------- 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: 0.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 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: 0.7820 moved from start: 0.1791 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= 0.202 Angle : 0.525 5.947 15439 Z= 0.286 Chirality : 0.038 0.132 1803 Planarity : 0.004 0.030 1598 Dihedral : 23.736 153.048 2423 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.75 % Allowed : 11.06 % Favored : 88.18 % 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: 0.42 (0.27), residues: 1067 helix: 1.11 (0.24), residues: 499 sheet: -1.25 (0.29), residues: 278 loop : 0.82 (0.42), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.005 0.001 HIS H 58 PHE 0.008 0.002 PHE D 132 TYR 0.005 0.001 TYR F 36 ARG 0.006 0.000 ARG F 67 *********************** 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 172 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 1.196 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 170 average time/residue: 0.3592 time to fit residues: 77.1415 Evaluate side-chains 163 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0952 time to fit residues: 2.0038 ------------------------------------------------------------------------------- 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: 0.9990 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 0.0170 chunk 60 optimal weight: 0.0270 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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: 0.7803 moved from start: 0.1851 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= 0.170 Angle : 0.514 5.672 15439 Z= 0.284 Chirality : 0.037 0.133 1803 Planarity : 0.004 0.032 1598 Dihedral : 23.688 152.838 2423 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.64 % Allowed : 11.49 % Favored : 87.86 % 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: 0.43 (0.27), residues: 1067 helix: 1.10 (0.24), residues: 501 sheet: -1.25 (0.29), residues: 278 loop : 0.86 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.003 0.001 HIS H 58 PHE 0.007 0.002 PHE F 63 TYR 0.005 0.000 TYR F 36 ARG 0.007 0.000 ARG F 67 *********************** 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 167 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 161 time to evaluate : 1.178 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 163 average time/residue: 0.3803 time to fit residues: 78.9936 Evaluate side-chains 165 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 161 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3265 time to fit residues: 2.9707 ------------------------------------------------------------------------------- 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: 0.8980 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 0.0010 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** 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: 0.1883 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= 0.183 Angle : 0.522 5.842 15439 Z= 0.286 Chirality : 0.037 0.173 1803 Planarity : 0.004 0.044 1598 Dihedral : 23.686 152.840 2423 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.32 % Allowed : 11.60 % Favored : 88.08 % 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: 0.43 (0.27), residues: 1067 helix: 1.10 (0.24), residues: 501 sheet: -1.23 (0.29), residues: 278 loop : 0.85 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.004 0.001 HIS H 58 PHE 0.007 0.002 PHE E 132 TYR 0.005 0.001 TYR F 36 ARG 0.007 0.000 ARG F 67 ********************** 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 165 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 1.109 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 162 average time/residue: 0.3723 time to fit residues: 75.6520 Evaluate side-chains 161 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1152 time to fit residues: 1.6041 ------------------------------------------------------------------------------- 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: 0.2980 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 0.0570 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** 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 = 0.4194 r_free = 0.4194 target = 0.183885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130482 restraints weight = 11257.245| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.15 r_work: 0.3308 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1916 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= 0.178 Angle : 0.520 5.676 15439 Z= 0.285 Chirality : 0.037 0.132 1803 Planarity : 0.004 0.032 1598 Dihedral : 23.659 152.732 2423 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.32 % Allowed : 11.92 % Favored : 87.76 % 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: 1.05 (0.24), residues: 507 sheet: -1.23 (0.29), residues: 278 loop : 0.65 (0.43), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 135 HIS 0.004 0.001 HIS H 58 PHE 0.007 0.002 PHE F 63 TYR 0.005 0.000 TYR F 36 ARG 0.011 0.000 ARG F 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.57 seconds wall clock time: 51 minutes 47.71 seconds (3107.71 seconds total)