Starting phenix.real_space_refine on Wed Apr 10 05:59:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl9_12461/04_2024/7nl9_12461.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl9_12461/04_2024/7nl9_12461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl9_12461/04_2024/7nl9_12461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl9_12461/04_2024/7nl9_12461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl9_12461/04_2024/7nl9_12461.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl9_12461/04_2024/7nl9_12461.pdb" } resolution = 2.86 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= 0.001 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 S 30 5.16 5 C 6090 2.51 5 N 1513 2.21 5 O 1623 1.98 5 H 9500 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 233": "OD1" <-> "OD2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "P ASP 32": "OD1" <-> "OD2" Residue "P PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "a PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 222": "OD1" <-> "OD2" Residue "b GLU 76": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18756 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 137 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 2, 'TRANS': 5} Chain: "G" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 631 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Chain breaks: 2 Chain: "H" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1562 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 3 Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 979 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "d" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 952 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Time building chain proxies: 9.06, per 1000 atoms: 0.48 Number of scatterers: 18756 At special positions: 0 Unit cell: (95.45, 77.19, 116.2, 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 30 16.00 O 1623 8.00 N 1513 7.00 C 6090 6.00 H 9500 1.00 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: 17.01 Conformation dependent library (CDL) restraints added in 1.9 seconds 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2186 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 80.5% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'G' and resid 53 through 61 Processing helix chain 'G' and resid 227 through 236 removed outlier: 3.520A pdb=" N LEU G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 105 through 118 Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.524A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 80 removed outlier: 4.040A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.448A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 removed outlier: 3.545A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 80 removed outlier: 4.349A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.524A pdb=" N ILE M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 Processing helix chain 'N' and resid 49 through 80 removed outlier: 4.563A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.525A pdb=" N ALA N 66 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 removed outlier: 3.504A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 80 removed outlier: 4.699A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.984A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.732A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 81 removed outlier: 3.676A pdb=" N PHE P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.589A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 50 Processing helix chain 'Q' and resid 51 through 52 No H-bonds generated for 'chain 'Q' and resid 51 through 52' Processing helix chain 'Q' and resid 53 through 80 Processing helix chain 'R' and resid 4 through 46 removed outlier: 3.572A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 81 removed outlier: 4.030A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 3.673A pdb=" N ALA R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 46 Processing helix chain 'S' and resid 49 through 81 removed outlier: 4.476A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.644A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 81 removed outlier: 4.050A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 4.192A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 51 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.571A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.501A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 204 Proline residue: a 182 - end of helix removed outlier: 3.866A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 5.760A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.778A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 49 removed outlier: 3.624A pdb=" N VAL b 49 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 84 removed outlier: 3.563A pdb=" N ALA b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN b 82 " --> pdb=" O VAL b 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 61 Processing sheet with id=AA1, first strand: chain 'C' and resid 539 through 540 Processing sheet with id=AA2, first strand: chain 'G' and resid 223 through 224 removed outlier: 6.379A pdb=" N SER G 223 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N GLN H 44 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 31 through 34 removed outlier: 4.168A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AA5, first strand: chain 'a' and resid 112 through 114 840 hydrogen bonds defined for protein. 2496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.18 Time building geometry restraints manager: 17.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9499 1.03 - 1.23: 2 1.23 - 1.42: 3828 1.42 - 1.61: 5551 1.61 - 1.81: 59 Bond restraints: 18939 Sorted by residual: bond pdb=" CA VAL d 23 " pdb=" CB VAL d 23 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.72e-01 bond pdb=" N GLN L 46 " pdb=" CA GLN L 46 " ideal model delta sigma weight residual 1.463 1.455 0.008 9.30e-03 1.16e+04 7.49e-01 bond pdb=" CB MET T 21 " pdb=" CG MET T 21 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.42e-01 bond pdb=" CB ASN R 71 " pdb=" CG ASN R 71 " ideal model delta sigma weight residual 1.516 1.501 0.015 2.50e-02 1.60e+03 3.64e-01 bond pdb=" C GLN R 46 " pdb=" O GLN R 46 " ideal model delta sigma weight residual 1.249 1.244 0.005 8.50e-03 1.38e+04 3.61e-01 ... (remaining 18934 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.82: 302 106.82 - 113.61: 22590 113.61 - 120.41: 6547 120.41 - 127.20: 4842 127.20 - 134.00: 88 Bond angle restraints: 34369 Sorted by residual: angle pdb=" C CYS a 144 " pdb=" N TYR a 145 " pdb=" CA TYR a 145 " ideal model delta sigma weight residual 121.14 115.94 5.20 1.75e+00 3.27e-01 8.83e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 118.74 -4.84 1.80e+00 3.09e-01 7.24e+00 angle pdb=" N TYR a 145 " pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " ideal model delta sigma weight residual 110.40 113.94 -3.54 1.63e+00 3.76e-01 4.73e+00 angle pdb=" N GLY Q 62 " pdb=" CA GLY Q 62 " pdb=" C GLY Q 62 " ideal model delta sigma weight residual 113.18 109.19 3.99 2.37e+00 1.78e-01 2.83e+00 angle pdb=" C LEU b 39 " pdb=" N ILE b 40 " pdb=" CA ILE b 40 " ideal model delta sigma weight residual 120.46 118.24 2.22 1.37e+00 5.33e-01 2.62e+00 ... (remaining 34364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 7661 16.70 - 33.40: 733 33.40 - 50.10: 206 50.10 - 66.80: 242 66.80 - 83.50: 3 Dihedral angle restraints: 8845 sinusoidal: 4753 harmonic: 4092 Sorted by residual: dihedral pdb=" CA GLU G 225 " pdb=" C GLU G 225 " pdb=" N PRO G 226 " pdb=" CA PRO G 226 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA GLN L 46 " pdb=" C GLN L 46 " pdb=" N PRO L 47 " pdb=" CA PRO L 47 " ideal model delta harmonic sigma weight residual 180.00 -164.70 -15.30 0 5.00e+00 4.00e-02 9.36e+00 dihedral pdb=" N ARG H 78 " pdb=" CA ARG H 78 " pdb=" CB ARG H 78 " pdb=" CG ARG H 78 " ideal model delta sinusoidal sigma weight residual -60.00 -113.95 53.95 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 8842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 956 0.029 - 0.059: 311 0.059 - 0.088: 192 0.088 - 0.117: 50 0.117 - 0.146: 6 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CA PRO H 36 " pdb=" N PRO H 36 " pdb=" C PRO H 36 " pdb=" CB PRO H 36 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA VAL H 77 " pdb=" N VAL H 77 " pdb=" C VAL H 77 " pdb=" CB VAL H 77 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE a 81 " pdb=" N ILE a 81 " pdb=" C ILE a 81 " pdb=" CB ILE a 81 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 1512 not shown) Planarity restraints: 2834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 35 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO H 36 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 36 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 36 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 52 " 0.142 9.50e-02 1.11e+02 4.74e-02 2.51e+00 pdb=" NE ARG R 52 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG R 52 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG R 52 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 52 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG R 52 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG R 52 " 0.003 2.00e-02 2.50e+03 pdb="HH21 ARG R 52 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG R 52 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 66 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C ALA Q 66 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA Q 66 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA Q 67 " 0.009 2.00e-02 2.50e+03 ... (remaining 2831 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1310 2.22 - 2.81: 40705 2.81 - 3.41: 55678 3.41 - 4.00: 73369 4.00 - 4.60: 114251 Nonbonded interactions: 285313 Sorted by model distance: nonbonded pdb=" OE1 GLU N 48 " pdb=" H GLU N 48 " model vdw 1.619 1.850 nonbonded pdb=" OE2 GLU G 225 " pdb="HH22 ARG L 45 " model vdw 1.656 1.850 nonbonded pdb="HE22 GLN O 86 " pdb=" OD2 ASP P 4 " model vdw 1.657 1.850 nonbonded pdb=" O ASN O 6 " pdb=" HG1 THR O 10 " model vdw 1.682 1.850 nonbonded pdb=" OE1 GLU O 48 " pdb=" H GLU O 48 " model vdw 1.689 1.850 ... (remaining 285308 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 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.810 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: 0.310 Extract box with map and model: 25.210 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 65.750 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 0.024 9439 Z= 0.169 Angle : 0.475 5.200 12819 Z= 0.261 Chirality : 0.039 0.146 1515 Planarity : 0.005 0.062 1645 Dihedral : 13.117 83.497 3218 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1229 helix: 1.24 (0.17), residues: 980 sheet: -0.83 (0.82), residues: 32 loop : 0.98 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.018 0.001 PHE L 69 TYR 0.011 0.001 TYR a 145 ARG 0.006 0.001 ARG Q 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: H 47 ASP cc_start: 0.8184 (m-30) cc_final: 0.7869 (m-30) REVERT: M 46 GLN cc_start: 0.8081 (mp10) cc_final: 0.7865 (mp10) outliers start: 0 outliers final: 1 residues processed: 131 average time/residue: 2.5876 time to fit residues: 365.5751 Evaluate side-chains 87 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 0.0970 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9439 Z= 0.218 Angle : 0.508 5.156 12819 Z= 0.276 Chirality : 0.040 0.154 1515 Planarity : 0.004 0.057 1645 Dihedral : 3.840 24.725 1307 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.23 % Allowed : 8.71 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.24), residues: 1229 helix: 2.19 (0.17), residues: 985 sheet: -1.00 (0.80), residues: 34 loop : 1.08 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS a 158 PHE 0.013 0.002 PHE M 58 TYR 0.029 0.001 TYR a 145 ARG 0.004 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 65 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7768 (mm-30) outliers start: 11 outliers final: 6 residues processed: 99 average time/residue: 2.5952 time to fit residues: 277.2807 Evaluate side-chains 88 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain S residue 86 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 0.0030 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9439 Z= 0.253 Angle : 0.499 5.115 12819 Z= 0.270 Chirality : 0.039 0.163 1515 Planarity : 0.004 0.050 1645 Dihedral : 3.905 26.225 1307 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.56 % Allowed : 9.82 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.24), residues: 1229 helix: 2.49 (0.16), residues: 987 sheet: -0.98 (0.82), residues: 34 loop : 0.92 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS a 158 PHE 0.014 0.001 PHE M 58 TYR 0.025 0.001 TYR a 145 ARG 0.004 0.000 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6742 (mtt-85) REVERT: M 65 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7725 (mm-30) REVERT: Q 75 MET cc_start: 0.8559 (ttp) cc_final: 0.8344 (ttp) REVERT: d 33 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6943 (tt0) outliers start: 14 outliers final: 6 residues processed: 92 average time/residue: 2.6714 time to fit residues: 264.9789 Evaluate side-chains 89 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9439 Z= 0.241 Angle : 0.496 5.065 12819 Z= 0.268 Chirality : 0.039 0.161 1515 Planarity : 0.004 0.049 1645 Dihedral : 3.845 16.400 1305 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.67 % Allowed : 10.71 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.24), residues: 1229 helix: 2.65 (0.16), residues: 987 sheet: -1.02 (0.81), residues: 34 loop : 0.98 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS a 158 PHE 0.015 0.001 PHE M 58 TYR 0.024 0.001 TYR a 145 ARG 0.004 0.000 ARG Q 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6746 (mtt-85) REVERT: M 65 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7682 (mm-30) REVERT: d 43 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7494 (mm-30) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 2.7153 time to fit residues: 265.9889 Evaluate side-chains 90 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9439 Z= 0.308 Angle : 0.512 5.089 12819 Z= 0.279 Chirality : 0.040 0.176 1515 Planarity : 0.004 0.053 1645 Dihedral : 3.950 16.147 1305 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.67 % Allowed : 11.94 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.24), residues: 1229 helix: 2.61 (0.16), residues: 987 sheet: -1.09 (0.82), residues: 34 loop : 0.93 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS H 38 PHE 0.016 0.002 PHE a 142 TYR 0.021 0.001 TYR a 145 ARG 0.005 0.000 ARG Q 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6737 (mtt-85) REVERT: Q 75 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8332 (ttp) REVERT: d 33 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.7036 (mt0) outliers start: 15 outliers final: 8 residues processed: 91 average time/residue: 2.8267 time to fit residues: 276.3323 Evaluate side-chains 89 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9439 Z= 0.267 Angle : 0.505 5.024 12819 Z= 0.273 Chirality : 0.039 0.166 1515 Planarity : 0.004 0.051 1645 Dihedral : 3.940 16.343 1305 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.01 % Allowed : 12.28 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.24), residues: 1229 helix: 2.64 (0.16), residues: 987 sheet: -1.23 (0.80), residues: 34 loop : 0.94 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE M 58 TYR 0.021 0.001 TYR a 145 ARG 0.002 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6731 (mtt-85) REVERT: Q 75 MET cc_start: 0.8572 (ttp) cc_final: 0.8298 (ttp) REVERT: d 33 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.7073 (mt0) outliers start: 18 outliers final: 8 residues processed: 93 average time/residue: 2.5911 time to fit residues: 259.7127 Evaluate side-chains 86 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9439 Z= 0.294 Angle : 0.510 5.043 12819 Z= 0.277 Chirality : 0.040 0.173 1515 Planarity : 0.004 0.052 1645 Dihedral : 3.969 16.126 1305 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.90 % Allowed : 12.95 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.24), residues: 1229 helix: 2.59 (0.16), residues: 987 sheet: -1.20 (0.80), residues: 34 loop : 0.90 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.002 PHE a 142 TYR 0.021 0.001 TYR a 145 ARG 0.002 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6697 (mtt-85) REVERT: L 48 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8006 (mm-30) REVERT: d 33 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.7030 (mt0) outliers start: 17 outliers final: 9 residues processed: 88 average time/residue: 2.6518 time to fit residues: 251.3961 Evaluate side-chains 88 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 48 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.0970 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9439 Z= 0.241 Angle : 0.499 5.058 12819 Z= 0.269 Chirality : 0.039 0.161 1515 Planarity : 0.004 0.050 1645 Dihedral : 3.928 16.364 1305 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.79 % Allowed : 13.62 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.24), residues: 1229 helix: 2.67 (0.16), residues: 987 sheet: -1.17 (0.79), residues: 34 loop : 0.93 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.015 0.001 PHE M 58 TYR 0.020 0.001 TYR a 145 ARG 0.003 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6675 (mtt-85) REVERT: Q 75 MET cc_start: 0.8575 (ttp) cc_final: 0.8347 (ttp) REVERT: d 33 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.7028 (mt0) outliers start: 16 outliers final: 9 residues processed: 87 average time/residue: 2.6463 time to fit residues: 248.2482 Evaluate side-chains 86 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9439 Z= 0.273 Angle : 0.508 5.031 12819 Z= 0.275 Chirality : 0.039 0.169 1515 Planarity : 0.004 0.051 1645 Dihedral : 3.939 15.943 1305 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.34 % Allowed : 13.73 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.24), residues: 1229 helix: 2.64 (0.16), residues: 987 sheet: -1.17 (0.80), residues: 34 loop : 0.91 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE a 142 TYR 0.020 0.001 TYR a 145 ARG 0.002 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6678 (mtt-85) REVERT: Q 75 MET cc_start: 0.8569 (ttp) cc_final: 0.8324 (ttp) REVERT: d 33 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.7012 (mt0) outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 2.7381 time to fit residues: 247.7506 Evaluate side-chains 85 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 71 ASN ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9439 Z= 0.250 Angle : 0.502 5.038 12819 Z= 0.271 Chirality : 0.039 0.164 1515 Planarity : 0.004 0.051 1645 Dihedral : 3.927 16.137 1305 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.56 % Allowed : 13.73 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.24), residues: 1229 helix: 2.67 (0.16), residues: 987 sheet: -1.16 (0.79), residues: 34 loop : 0.92 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE M 58 TYR 0.020 0.001 TYR a 145 ARG 0.004 0.000 ARG N 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 105 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6680 (mtt-85) REVERT: Q 75 MET cc_start: 0.8559 (ttp) cc_final: 0.8323 (ttp) REVERT: d 33 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.7000 (mt0) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 2.6023 time to fit residues: 238.8654 Evaluate side-chains 85 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain S residue 86 GLN Chi-restraints excluded: chain b residue 25 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain d residue 35 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.078988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.064050 restraints weight = 53861.920| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.94 r_work: 0.2817 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9439 Z= 0.244 Angle : 0.499 5.992 12819 Z= 0.269 Chirality : 0.039 0.163 1515 Planarity : 0.004 0.050 1645 Dihedral : 3.912 16.034 1305 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.34 % Allowed : 13.73 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.24), residues: 1229 helix: 2.70 (0.16), residues: 987 sheet: -1.12 (0.80), residues: 34 loop : 0.90 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE M 74 TYR 0.020 0.001 TYR a 145 ARG 0.004 0.000 ARG N 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6211.84 seconds wall clock time: 110 minutes 59.96 seconds (6659.96 seconds total)