Starting phenix.real_space_refine on Mon Apr 8 01:49:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgb_22320/04_2024/7jgb_22320.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgb_22320/04_2024/7jgb_22320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgb_22320/04_2024/7jgb_22320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgb_22320/04_2024/7jgb_22320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgb_22320/04_2024/7jgb_22320.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgb_22320/04_2024/7jgb_22320.pdb" } resolution = 3.5 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= -0.006 sd= 0.141 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4941 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 4847 2.51 5 N 1174 2.21 5 O 1214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a ARG 50": "NH1" <-> "NH2" Residue "a GLU 67": "OE1" <-> "OE2" Residue "a TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 188": "NH1" <-> "NH2" Residue "a PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 222": "OD1" <-> "OD2" Residue "a GLU 246": "OE1" <-> "OE2" Residue "b PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "1 ARG 45": "NH1" <-> "NH2" Residue "3 GLU 48": "OE1" <-> "OE2" Residue "3 GLU 65": "OE1" <-> "OE2" Residue "4 ASP 32": "OD1" <-> "OD2" Residue "4 GLU 65": "OE1" <-> "OE2" Residue "5 ASP 32": "OD1" <-> "OD2" Residue "5 GLU 65": "OE1" <-> "OE2" Residue "6 ARG 45": "NH1" <-> "NH2" Residue "7 ASP 32": "OD1" <-> "OD2" Residue "7 GLU 65": "OE1" <-> "OE2" Residue "8 ASP 32": "OD1" <-> "OD2" Residue "9 GLU 65": "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: 7261 Number of models: 1 Model: "" Number of chains: 12 Chain: "a" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1602 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 341 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 41} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 37} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 552 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "3" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 548 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "4" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 550 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "6" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "7" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "8" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 569 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 78} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "9" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.62, per 1000 atoms: 0.64 Number of scatterers: 7261 At special positions: 0 Unit cell: (79.31, 94.76, 88.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1214 8.00 N 1174 7.00 C 4847 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: 3.05 Conformation dependent library (CDL) restraints added in 1.4 seconds 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'a' and resid 32 through 53 removed outlier: 3.812A pdb=" N THR a 38 " --> pdb=" O ALA a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 81 removed outlier: 3.657A pdb=" N TRP a 66 " --> pdb=" O VAL a 62 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN a 72 " --> pdb=" O ALA a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 106 removed outlier: 4.102A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE a 100 " --> pdb=" O ILE a 96 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER a 103 " --> pdb=" O PHE a 99 " (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: 3.680A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE a 140 " --> pdb=" O ALA a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.907A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 203 removed outlier: 3.965A pdb=" N VAL a 176 " --> pdb=" O PRO a 172 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU a 179 " --> pdb=" O ILE a 175 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 4.002A pdb=" N ARG a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 204 through 206 No H-bonds generated for 'chain 'a' and resid 204 through 206' Processing helix chain 'a' and resid 207 through 246 removed outlier: 4.866A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.840A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU a 246 " --> pdb=" O SER a 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 49 removed outlier: 4.295A pdb=" N ALA b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL b 41 " --> pdb=" O ILE b 37 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 64 Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 39 Processing helix chain '1' and resid 6 through 46 Processing helix chain '1' and resid 49 through 81 removed outlier: 4.272A pdb=" N THR 1 55 " --> pdb=" O GLY 1 51 " (cutoff:3.500A) Proline residue: 1 56 - end of helix Processing helix chain '2' and resid 6 through 46 Processing helix chain '2' and resid 49 through 80 removed outlier: 4.569A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix Processing helix chain '3' and resid 6 through 46 Processing helix chain '3' and resid 49 through 81 removed outlier: 4.759A pdb=" N THR 3 55 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) Proline residue: 3 56 - end of helix removed outlier: 3.770A pdb=" N ALA 3 67 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 46 removed outlier: 3.710A pdb=" N ARG 4 45 " --> pdb=" O SER 4 41 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 80 removed outlier: 5.220A pdb=" N THR 4 55 " --> pdb=" O GLY 4 51 " (cutoff:3.500A) Proline residue: 4 56 - end of helix removed outlier: 3.685A pdb=" N ALA 4 67 " --> pdb=" O LEU 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 46 Processing helix chain '5' and resid 49 through 81 Proline residue: 5 56 - end of helix Processing helix chain '6' and resid 6 through 46 removed outlier: 3.550A pdb=" N ALA 6 38 " --> pdb=" O ILE 6 34 " (cutoff:3.500A) Processing helix chain '6' and resid 47 through 53 removed outlier: 4.157A pdb=" N GLY 6 51 " --> pdb=" O PRO 6 47 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 81 removed outlier: 3.962A pdb=" N ALA 6 67 " --> pdb=" O LEU 6 63 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 46 removed outlier: 3.572A pdb=" N ALA 7 38 " --> pdb=" O ILE 7 34 " (cutoff:3.500A) Processing helix chain '7' and resid 49 through 82 removed outlier: 4.376A pdb=" N THR 7 55 " --> pdb=" O GLY 7 51 " (cutoff:3.500A) Proline residue: 7 56 - end of helix Processing helix chain '8' and resid 4 through 46 removed outlier: 3.568A pdb=" N ILE 8 8 " --> pdb=" O ASP 8 4 " (cutoff:3.500A) Processing helix chain '8' and resid 49 through 82 removed outlier: 4.432A pdb=" N THR 8 55 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) Proline residue: 8 56 - end of helix Processing helix chain '9' and resid 6 through 46 Processing helix chain '9' and resid 49 through 81 removed outlier: 4.066A pdb=" N THR 9 55 " --> pdb=" O GLY 9 51 " (cutoff:3.500A) Proline residue: 9 56 - end of helix removed outlier: 3.617A pdb=" N ALA 9 66 " --> pdb=" O GLY 9 62 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN 9 71 " --> pdb=" O ALA 9 67 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 2190 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: 2.39 Time building geometry restraints manager: 3.30 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: 2272 1.34 - 1.46: 1682 1.46 - 1.58: 3416 1.58 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 7421 Sorted by residual: bond pdb=" N GLY b 20 " pdb=" CA GLY b 20 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.32e+00 bond pdb=" CG ARG d 38 " pdb=" CD ARG d 38 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.24e+00 bond pdb=" CB VAL b 56 " pdb=" CG1 VAL b 56 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.94e+00 bond pdb=" CB LYS b 55 " pdb=" CG LYS b 55 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CB ILE 2 43 " pdb=" CG2 ILE 2 43 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.48e+00 ... (remaining 7416 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.35: 222 106.35 - 113.30: 3980 113.30 - 120.25: 2975 120.25 - 127.21: 2847 127.21 - 134.16: 63 Bond angle restraints: 10087 Sorted by residual: angle pdb=" N THR 4 82 " pdb=" CA THR 4 82 " pdb=" C THR 4 82 " ideal model delta sigma weight residual 109.57 113.62 -4.05 1.23e+00 6.61e-01 1.08e+01 angle pdb=" C ALA 4 81 " pdb=" N THR 4 82 " pdb=" CA THR 4 82 " ideal model delta sigma weight residual 120.83 124.76 -3.93 1.43e+00 4.89e-01 7.54e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 118.07 -4.17 1.80e+00 3.09e-01 5.36e+00 angle pdb=" CA TRP a 208 " pdb=" CB TRP a 208 " pdb=" CG TRP a 208 " ideal model delta sigma weight residual 113.60 117.56 -3.96 1.90e+00 2.77e-01 4.34e+00 angle pdb=" N PHE a 133 " pdb=" CA PHE a 133 " pdb=" CB PHE a 133 " ideal model delta sigma weight residual 110.16 107.14 3.02 1.48e+00 4.57e-01 4.17e+00 ... (remaining 10082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3814 17.92 - 35.83: 299 35.83 - 53.75: 37 53.75 - 71.66: 10 71.66 - 89.58: 7 Dihedral angle restraints: 4167 sinusoidal: 1423 harmonic: 2744 Sorted by residual: dihedral pdb=" CA GLN 4 46 " pdb=" C GLN 4 46 " pdb=" N PRO 4 47 " pdb=" CA PRO 4 47 " ideal model delta harmonic sigma weight residual -180.00 -156.86 -23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ARG d 38 " pdb=" C ARG d 38 " pdb=" N ALA d 39 " pdb=" CA ALA d 39 " ideal model delta harmonic sigma weight residual -180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA VAL b 49 " pdb=" C VAL b 49 " pdb=" N VAL b 50 " pdb=" CA VAL b 50 " ideal model delta harmonic sigma weight residual -180.00 -161.31 -18.69 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 4164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 711 0.032 - 0.064: 321 0.064 - 0.096: 139 0.096 - 0.128: 26 0.128 - 0.160: 7 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CA PRO 5 47 " pdb=" N PRO 5 47 " pdb=" C PRO 5 47 " pdb=" CB PRO 5 47 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA PRO 4 47 " pdb=" N PRO 4 47 " pdb=" C PRO 4 47 " pdb=" CB PRO 4 47 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA PRO 3 47 " pdb=" N PRO 3 47 " pdb=" C PRO 3 47 " pdb=" CB PRO 3 47 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1201 not shown) Planarity restraints: 1271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL b 50 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO b 51 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO b 51 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO b 51 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE d 18 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.71e+00 pdb=" C ILE d 18 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE d 18 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL d 19 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 208 " -0.017 2.00e-02 2.50e+03 1.07e-02 2.88e+00 pdb=" CG TRP a 208 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP a 208 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP a 208 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP a 208 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 208 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP a 208 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 208 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 208 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP a 208 " -0.003 2.00e-02 2.50e+03 ... (remaining 1268 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 2875 2.88 - 3.38: 8228 3.38 - 3.89: 12291 3.89 - 4.39: 13946 4.39 - 4.90: 23299 Nonbonded interactions: 60639 Sorted by model distance: nonbonded pdb=" OG SER a 80 " pdb=" OG SER a 242 " model vdw 2.372 2.440 nonbonded pdb=" O ARG d 38 " pdb=" N ALA d 40 " model vdw 2.402 2.520 nonbonded pdb=" O PHE 9 78 " pdb=" OG1 THR 9 82 " model vdw 2.435 2.440 nonbonded pdb=" OH TYR 4 68 " pdb=" OD1 ASN 5 71 " model vdw 2.438 2.440 nonbonded pdb=" OG SER 8 41 " pdb=" NH1 ARG 8 45 " model vdw 2.441 2.520 ... (remaining 60634 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 '1' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '2' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 84)) selection = (chain '3' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '4' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 84)) selection = (chain '6' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '7' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '8' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '9' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 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: 0.000 Extract box with map and model: 6.880 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.070 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 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 : 0.007 0.057 7421 Z= 0.448 Angle : 0.644 6.339 10087 Z= 0.390 Chirality : 0.043 0.160 1204 Planarity : 0.005 0.052 1271 Dihedral : 13.529 89.580 2447 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.45 % Allowed : 5.80 % Favored : 93.75 % 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: -0.15 (0.25), residues: 996 helix: 0.30 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -2.59 (0.52), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP a 208 HIS 0.003 0.001 HIS a 158 PHE 0.025 0.002 PHE a 99 TYR 0.021 0.003 TYR a 48 ARG 0.004 0.001 ARG 3 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: a 188 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8012 (ttm-80) REVERT: 3 78 PHE cc_start: 0.6786 (m-10) cc_final: 0.6573 (m-10) REVERT: 4 54 PHE cc_start: 0.6436 (OUTLIER) cc_final: 0.5703 (m-10) REVERT: 5 75 MET cc_start: 0.7528 (ttp) cc_final: 0.7023 (ttp) REVERT: 6 41 SER cc_start: 0.8183 (m) cc_final: 0.7902 (t) REVERT: 7 75 MET cc_start: 0.7162 (tmm) cc_final: 0.6631 (tmm) outliers start: 3 outliers final: 2 residues processed: 112 average time/residue: 0.1617 time to fit residues: 26.3008 Evaluate side-chains 110 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 7 residue 55 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.5980 chunk 75 optimal weight: 0.0270 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 32 ASN 5 6 ASN 9 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7421 Z= 0.230 Angle : 0.568 7.938 10087 Z= 0.298 Chirality : 0.041 0.137 1204 Planarity : 0.005 0.046 1271 Dihedral : 4.649 44.825 1054 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.23 % Allowed : 11.90 % Favored : 85.86 % 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: 2.61 (0.27), residues: 996 helix: 2.14 (0.17), residues: 872 sheet: None (None), residues: 0 loop : -1.37 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 212 HIS 0.002 0.001 HIS a 146 PHE 0.021 0.001 PHE a 221 TYR 0.015 0.001 TYR a 145 ARG 0.005 0.000 ARG d 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: a 64 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7143 (mt) REVERT: 3 78 PHE cc_start: 0.6576 (m-10) cc_final: 0.6342 (m-10) REVERT: 4 54 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.6046 (m-10) REVERT: 5 75 MET cc_start: 0.7569 (ttp) cc_final: 0.6915 (ttp) REVERT: 6 41 SER cc_start: 0.8264 (m) cc_final: 0.7875 (t) REVERT: 7 75 MET cc_start: 0.7305 (tmm) cc_final: 0.7084 (tmm) outliers start: 15 outliers final: 11 residues processed: 120 average time/residue: 0.1476 time to fit residues: 25.9318 Evaluate side-chains 125 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 3 residue 10 THR Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 6 ASN Chi-restraints excluded: chain 7 residue 6 ASN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 10 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7421 Z= 0.256 Angle : 0.565 7.153 10087 Z= 0.296 Chirality : 0.041 0.140 1204 Planarity : 0.005 0.043 1271 Dihedral : 4.571 48.779 1053 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.98 % Allowed : 14.43 % Favored : 82.59 % 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: 3.27 (0.27), residues: 996 helix: 2.59 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -1.14 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 208 HIS 0.002 0.001 HIS a 146 PHE 0.018 0.001 PHE a 221 TYR 0.016 0.002 TYR a 145 ARG 0.002 0.000 ARG 2 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: a 64 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7076 (mt) REVERT: a 112 GLN cc_start: 0.7102 (tt0) cc_final: 0.6889 (tt0) REVERT: 1 21 MET cc_start: 0.7825 (mmm) cc_final: 0.7416 (mmm) REVERT: 3 78 PHE cc_start: 0.6487 (m-10) cc_final: 0.6284 (m-10) REVERT: 4 46 GLN cc_start: 0.6530 (mm110) cc_final: 0.6308 (mm110) REVERT: 4 54 PHE cc_start: 0.6777 (OUTLIER) cc_final: 0.6255 (m-10) REVERT: 5 75 MET cc_start: 0.7647 (ttp) cc_final: 0.7009 (ttp) REVERT: 6 41 SER cc_start: 0.8289 (m) cc_final: 0.7939 (t) outliers start: 20 outliers final: 13 residues processed: 114 average time/residue: 0.1528 time to fit residues: 25.2464 Evaluate side-chains 121 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain a residue 243 GLN Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 3 residue 10 THR Chi-restraints excluded: chain 4 residue 6 ASN Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 7 residue 6 ASN Chi-restraints excluded: chain 7 residue 10 THR Chi-restraints excluded: chain 8 residue 10 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.0670 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7421 Z= 0.193 Angle : 0.531 7.577 10087 Z= 0.270 Chirality : 0.039 0.157 1204 Planarity : 0.004 0.040 1271 Dihedral : 4.280 47.935 1053 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.98 % Allowed : 16.52 % Favored : 80.51 % 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: 3.75 (0.27), residues: 996 helix: 2.92 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -1.07 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.015 0.001 PHE a 221 TYR 0.015 0.001 TYR a 145 ARG 0.005 0.000 ARG 6 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: a 45 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7470 (mt) REVERT: a 64 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7111 (mt) REVERT: 1 21 MET cc_start: 0.7914 (mmm) cc_final: 0.7680 (mmm) REVERT: 4 54 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.6261 (m-10) REVERT: 5 75 MET cc_start: 0.7646 (ttp) cc_final: 0.7083 (ttp) REVERT: 6 41 SER cc_start: 0.8301 (m) cc_final: 0.7957 (t) REVERT: 7 21 MET cc_start: 0.7312 (mmm) cc_final: 0.7064 (mmm) REVERT: 7 75 MET cc_start: 0.7479 (tmm) cc_final: 0.6695 (tmm) outliers start: 20 outliers final: 11 residues processed: 123 average time/residue: 0.1565 time to fit residues: 27.9203 Evaluate side-chains 126 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain a residue 243 GLN Chi-restraints excluded: chain 3 residue 10 THR Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 7 residue 6 ASN Chi-restraints excluded: chain 7 residue 10 THR Chi-restraints excluded: chain 7 residue 55 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 49 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7421 Z= 0.203 Angle : 0.531 7.235 10087 Z= 0.271 Chirality : 0.039 0.165 1204 Planarity : 0.004 0.039 1271 Dihedral : 4.144 48.054 1052 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.17 % Allowed : 16.96 % Favored : 78.87 % 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: 3.93 (0.27), residues: 996 helix: 3.02 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -0.87 (0.61), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.012 0.001 PHE a 221 TYR 0.016 0.001 TYR a 145 ARG 0.005 0.000 ARG d 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: a 45 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7489 (mt) REVERT: a 64 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7169 (mt) REVERT: 1 21 MET cc_start: 0.7935 (mmm) cc_final: 0.7492 (mmm) REVERT: 3 78 PHE cc_start: 0.6174 (m-10) cc_final: 0.5968 (m-10) REVERT: 4 54 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.6338 (m-10) REVERT: 5 21 MET cc_start: 0.6900 (tpt) cc_final: 0.6650 (tpt) REVERT: 5 75 MET cc_start: 0.7679 (ttp) cc_final: 0.7157 (ttp) REVERT: 6 41 SER cc_start: 0.8339 (m) cc_final: 0.7979 (t) REVERT: 7 75 MET cc_start: 0.7508 (tmm) cc_final: 0.6843 (tmm) outliers start: 28 outliers final: 19 residues processed: 130 average time/residue: 0.1466 time to fit residues: 27.7674 Evaluate side-chains 136 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain 1 residue 54 PHE Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 2 residue 58 PHE Chi-restraints excluded: chain 3 residue 10 THR Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 6 residue 64 VAL Chi-restraints excluded: chain 7 residue 6 ASN Chi-restraints excluded: chain 7 residue 10 THR Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 10 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 23 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7421 Z= 0.232 Angle : 0.550 7.654 10087 Z= 0.280 Chirality : 0.040 0.183 1204 Planarity : 0.004 0.039 1271 Dihedral : 4.205 48.186 1052 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.17 % Allowed : 16.82 % Favored : 79.02 % 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: 3.95 (0.27), residues: 996 helix: 3.02 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -0.77 (0.61), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.014 0.001 PHE 7 80 TYR 0.017 0.001 TYR a 145 ARG 0.006 0.000 ARG 6 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: a 45 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7498 (mt) REVERT: a 64 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7210 (mt) REVERT: 1 21 MET cc_start: 0.7944 (mmm) cc_final: 0.7494 (mmm) REVERT: 1 71 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.6905 (t0) REVERT: 3 78 PHE cc_start: 0.6054 (m-10) cc_final: 0.5839 (m-10) REVERT: 4 54 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.6274 (m-10) REVERT: 5 75 MET cc_start: 0.7758 (ttp) cc_final: 0.7063 (ttp) REVERT: 6 41 SER cc_start: 0.8379 (m) cc_final: 0.8009 (t) REVERT: 7 75 MET cc_start: 0.7518 (tmm) cc_final: 0.6804 (tmm) outliers start: 28 outliers final: 21 residues processed: 127 average time/residue: 0.1469 time to fit residues: 27.0015 Evaluate side-chains 138 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain a residue 243 GLN Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain 1 residue 54 PHE Chi-restraints excluded: chain 1 residue 71 ASN Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 2 residue 58 PHE Chi-restraints excluded: chain 3 residue 10 THR Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 6 residue 54 PHE Chi-restraints excluded: chain 6 residue 64 VAL Chi-restraints excluded: chain 7 residue 6 ASN Chi-restraints excluded: chain 7 residue 10 THR Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 10 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.0970 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7421 Z= 0.204 Angle : 0.561 9.458 10087 Z= 0.280 Chirality : 0.039 0.195 1204 Planarity : 0.004 0.039 1271 Dihedral : 4.128 47.568 1052 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.32 % Allowed : 17.71 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.10 (0.27), residues: 996 helix: 3.12 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -0.69 (0.62), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.012 0.001 PHE b 31 TYR 0.016 0.001 TYR a 145 ARG 0.008 0.000 ARG d 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: a 45 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7500 (mt) REVERT: a 64 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7188 (mt) REVERT: 1 21 MET cc_start: 0.7932 (mmm) cc_final: 0.7438 (mmm) REVERT: 4 54 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.6242 (m-10) REVERT: 5 75 MET cc_start: 0.7745 (ttp) cc_final: 0.7140 (ttp) REVERT: 6 41 SER cc_start: 0.8351 (m) cc_final: 0.7990 (t) REVERT: 7 75 MET cc_start: 0.7528 (tmm) cc_final: 0.6857 (tmm) REVERT: 8 75 MET cc_start: 0.7315 (tmm) cc_final: 0.7054 (tmm) outliers start: 29 outliers final: 23 residues processed: 126 average time/residue: 0.1531 time to fit residues: 28.1482 Evaluate side-chains 138 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain a residue 243 GLN Chi-restraints excluded: chain b residue 46 SER Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain 1 residue 54 PHE Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 58 PHE Chi-restraints excluded: chain 3 residue 10 THR Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 6 residue 54 PHE Chi-restraints excluded: chain 6 residue 64 VAL Chi-restraints excluded: chain 7 residue 6 ASN Chi-restraints excluded: chain 7 residue 10 THR Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 10 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 0.0670 chunk 84 optimal weight: 0.0010 chunk 89 optimal weight: 0.4980 overall best weight: 0.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7421 Z= 0.179 Angle : 0.560 9.431 10087 Z= 0.272 Chirality : 0.039 0.211 1204 Planarity : 0.004 0.041 1271 Dihedral : 3.998 46.411 1052 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.72 % Allowed : 18.15 % Favored : 78.12 % 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: 4.31 (0.27), residues: 996 helix: 3.27 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -0.64 (0.64), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.017 0.001 PHE 7 80 TYR 0.015 0.001 TYR a 145 ARG 0.009 0.000 ARG d 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 64 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7114 (mt) REVERT: 1 21 MET cc_start: 0.7917 (mmm) cc_final: 0.7449 (mmm) REVERT: 3 78 PHE cc_start: 0.5602 (m-10) cc_final: 0.5390 (m-10) REVERT: 4 54 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.6191 (m-10) REVERT: 5 75 MET cc_start: 0.7749 (ttp) cc_final: 0.7228 (ttp) REVERT: 6 41 SER cc_start: 0.8347 (m) cc_final: 0.7962 (t) REVERT: 7 75 MET cc_start: 0.7524 (tmm) cc_final: 0.6839 (tmm) REVERT: 8 75 MET cc_start: 0.7335 (tmm) cc_final: 0.7041 (tmm) outliers start: 25 outliers final: 21 residues processed: 123 average time/residue: 0.1487 time to fit residues: 26.6285 Evaluate side-chains 134 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain a residue 243 GLN Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain d residue 3 ILE Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain 1 residue 54 PHE Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 58 PHE Chi-restraints excluded: chain 3 residue 10 THR Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 6 residue 54 PHE Chi-restraints excluded: chain 6 residue 64 VAL Chi-restraints excluded: chain 7 residue 6 ASN Chi-restraints excluded: chain 7 residue 10 THR Chi-restraints excluded: chain 7 residue 59 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 0.0980 chunk 81 optimal weight: 0.1980 chunk 84 optimal weight: 0.0010 chunk 89 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 146 HIS ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7421 Z= 0.165 Angle : 0.547 8.490 10087 Z= 0.262 Chirality : 0.038 0.221 1204 Planarity : 0.004 0.042 1271 Dihedral : 3.821 44.068 1052 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.83 % Allowed : 19.35 % Favored : 77.83 % 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: 4.59 (0.27), residues: 996 helix: 3.44 (0.17), residues: 872 sheet: None (None), residues: 0 loop : -0.49 (0.64), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP a 212 HIS 0.003 0.001 HIS a 146 PHE 0.010 0.001 PHE 8 69 TYR 0.013 0.001 TYR a 145 ARG 0.011 0.001 ARG d 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 64 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7137 (tt) REVERT: 1 21 MET cc_start: 0.7910 (mmm) cc_final: 0.7455 (mmm) REVERT: 3 78 PHE cc_start: 0.5538 (m-10) cc_final: 0.5298 (m-10) REVERT: 4 54 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.6132 (m-10) REVERT: 4 80 PHE cc_start: 0.6651 (m-80) cc_final: 0.6435 (m-80) REVERT: 5 75 MET cc_start: 0.7692 (ttp) cc_final: 0.7209 (ttp) REVERT: 6 41 SER cc_start: 0.8327 (m) cc_final: 0.7934 (t) REVERT: 7 75 MET cc_start: 0.7460 (tmm) cc_final: 0.6981 (tmm) REVERT: 8 75 MET cc_start: 0.7339 (tmm) cc_final: 0.7044 (tmm) outliers start: 19 outliers final: 15 residues processed: 114 average time/residue: 0.1540 time to fit residues: 25.1993 Evaluate side-chains 122 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain a residue 243 GLN Chi-restraints excluded: chain 1 residue 54 PHE Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 2 residue 58 PHE Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 6 residue 43 ILE Chi-restraints excluded: chain 6 residue 54 PHE Chi-restraints excluded: chain 6 residue 64 VAL Chi-restraints excluded: chain 7 residue 10 THR Chi-restraints excluded: chain 7 residue 55 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 8 optimal weight: 0.0670 chunk 61 optimal weight: 0.3980 chunk 48 optimal weight: 0.0670 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 0.0770 chunk 24 optimal weight: 0.6980 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7421 Z= 0.167 Angle : 0.548 8.623 10087 Z= 0.263 Chirality : 0.038 0.234 1204 Planarity : 0.004 0.040 1271 Dihedral : 3.790 43.900 1052 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.12 % Allowed : 18.75 % Favored : 78.12 % 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: 4.62 (0.27), residues: 996 helix: 3.46 (0.17), residues: 872 sheet: None (None), residues: 0 loop : -0.43 (0.64), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 212 HIS 0.004 0.001 HIS a 146 PHE 0.020 0.001 PHE 7 80 TYR 0.015 0.001 TYR a 145 ARG 0.008 0.000 ARG 6 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: a 64 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7298 (mt) REVERT: 1 21 MET cc_start: 0.7924 (mmm) cc_final: 0.7453 (mmm) REVERT: 3 78 PHE cc_start: 0.5553 (m-10) cc_final: 0.5313 (m-10) REVERT: 4 54 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.6190 (m-10) REVERT: 5 75 MET cc_start: 0.7702 (ttp) cc_final: 0.7247 (ttp) REVERT: 6 41 SER cc_start: 0.8350 (m) cc_final: 0.7960 (t) REVERT: 7 75 MET cc_start: 0.7495 (tmm) cc_final: 0.6988 (tmm) REVERT: 8 75 MET cc_start: 0.7306 (tmm) cc_final: 0.7027 (tmm) outliers start: 21 outliers final: 18 residues processed: 112 average time/residue: 0.1657 time to fit residues: 26.6080 Evaluate side-chains 119 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain a residue 243 GLN Chi-restraints excluded: chain b residue 46 SER Chi-restraints excluded: chain d residue 3 ILE Chi-restraints excluded: chain 1 residue 54 PHE Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 2 residue 10 THR Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 58 PHE Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 6 residue 43 ILE Chi-restraints excluded: chain 6 residue 54 PHE Chi-restraints excluded: chain 6 residue 64 VAL Chi-restraints excluded: chain 7 residue 10 THR Chi-restraints excluded: chain 7 residue 55 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 57 optimal weight: 0.3980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.163402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.151747 restraints weight = 10429.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.154752 restraints weight = 5077.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.156575 restraints weight = 2931.911| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7421 Z= 0.193 Angle : 0.582 14.983 10087 Z= 0.277 Chirality : 0.039 0.228 1204 Planarity : 0.004 0.039 1271 Dihedral : 3.875 44.560 1052 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.42 % Allowed : 18.75 % Favored : 77.83 % 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: 4.52 (0.27), residues: 996 helix: 3.38 (0.17), residues: 872 sheet: None (None), residues: 0 loop : -0.41 (0.64), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 208 HIS 0.004 0.001 HIS a 146 PHE 0.013 0.001 PHE a 142 TYR 0.016 0.001 TYR a 145 ARG 0.008 0.000 ARG 6 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1537.73 seconds wall clock time: 28 minutes 57.83 seconds (1737.83 seconds total)