Starting phenix.real_space_refine on Fri Apr 5 21:42:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8scx_40346/04_2024/8scx_40346_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8scx_40346/04_2024/8scx_40346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8scx_40346/04_2024/8scx_40346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8scx_40346/04_2024/8scx_40346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8scx_40346/04_2024/8scx_40346_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8scx_40346/04_2024/8scx_40346_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 29 5.16 5 C 3659 2.51 5 N 992 2.21 5 O 1070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 413": "OE1" <-> "OE2" Residue "L GLU 129": "OE1" <-> "OE2" Residue "H ASP 77": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5753 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 978 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 971 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1947 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 82 Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 837 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 901 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} 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: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.69 Number of scatterers: 5753 At special positions: 0 Unit cell: (94.5, 75.6, 116.55, 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 29 16.00 P 3 15.00 O 1070 8.00 N 992 7.00 C 3659 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 114 " distance=2.03 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: 2.43 Conformation dependent library (CDL) restraints added in 1.3 seconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 8 sheets defined 48.9% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.708A pdb=" N ILE A 14 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 83 removed outlier: 4.037A pdb=" N ARG A 46 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLY A 47 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 48 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 52 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 55 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALA A 58 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.558A pdb=" N PHE A 65 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 67 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 69 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 70 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 71 " --> pdb=" O TRP A 68 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 75 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS A 77 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 83 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 108 through 137 Processing helix chain 'B' and resid 93 through 123 Processing helix chain 'B' and resid 130 through 170 Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 196 through 219 removed outlier: 3.772A pdb=" N TYR B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 125 Processing helix chain 'C' and resid 127 through 152 Proline residue: C 149 - end of helix Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.554A pdb=" N PHE C 265 " --> pdb=" O VAL C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 280 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 310 through 316 removed outlier: 3.758A pdb=" N LYS C 315 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 334 removed outlier: 3.614A pdb=" N GLU C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 108 No H-bonds generated for 'chain 'H' and resid 106 through 108' Processing helix chain 'H' and resid 119 through 121 No H-bonds generated for 'chain 'H' and resid 119 through 121' Processing sheet with id= A, first strand: chain 'C' and resid 337 through 339 removed outlier: 5.667A pdb=" N LYS C 379 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE C 385 " --> pdb=" O LYS C 379 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 342 through 347 removed outlier: 6.409A pdb=" N GLN C 372 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE C 346 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG C 370 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 421 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR C 403 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE C 419 " --> pdb=" O THR C 403 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.710A pdb=" N VAL C 366 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA C 354 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 364 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU C 356 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE C 362 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 24 through 27 removed outlier: 3.595A pdb=" N ASP L 94 " --> pdb=" O SER L 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER L 96 " --> pdb=" O SER L 89 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.178A pdb=" N LYS L 127 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL L 33 " --> pdb=" O LYS L 127 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU L 129 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLN L 61 " --> pdb=" O LEU L 70 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU L 70 " --> pdb=" O GLN L 61 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 22 through 27 Processing sheet with id= G, first strand: chain 'H' and resid 130 through 132 removed outlier: 3.504A pdb=" N ILE H 111 " --> pdb=" O GLN H 58 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY H 52 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER H 59 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU H 64 " --> pdb=" O SER H 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 115 through 117 removed outlier: 3.548A pdb=" N TYR H 125 " --> pdb=" O ARG H 116 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 924 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: 1.88 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1864 1.34 - 1.47: 1441 1.47 - 1.60: 2510 1.60 - 1.72: 6 1.72 - 1.85: 46 Bond restraints: 5867 Sorted by residual: bond pdb=" CA7 CDL A 301 " pdb=" OA8 CDL A 301 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.12e+02 bond pdb=" CB7 CDL A 301 " pdb=" OB8 CDL A 301 " ideal model delta sigma weight residual 1.334 1.448 -0.114 1.10e-02 8.26e+03 1.07e+02 bond pdb=" CA5 CDL A 301 " pdb=" OA6 CDL A 301 " ideal model delta sigma weight residual 1.342 1.450 -0.108 1.50e-02 4.44e+03 5.23e+01 bond pdb=" CB5 CDL A 301 " pdb=" OB6 CDL A 301 " ideal model delta sigma weight residual 1.342 1.447 -0.105 1.50e-02 4.44e+03 4.94e+01 bond pdb=" C8 PTY B 301 " pdb=" O7 PTY B 301 " ideal model delta sigma weight residual 1.331 1.453 -0.122 2.00e-02 2.50e+03 3.70e+01 ... (remaining 5862 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.45: 101 105.45 - 112.61: 3073 112.61 - 119.76: 1727 119.76 - 126.91: 2939 126.91 - 134.06: 74 Bond angle restraints: 7914 Sorted by residual: angle pdb=" C11 CDL A 301 " pdb=" CA5 CDL A 301 " pdb=" OA6 CDL A 301 " ideal model delta sigma weight residual 111.33 120.47 -9.14 1.32e+00 5.72e-01 4.78e+01 angle pdb=" C51 CDL A 301 " pdb=" CB5 CDL A 301 " pdb=" OB6 CDL A 301 " ideal model delta sigma weight residual 111.33 120.29 -8.96 1.32e+00 5.72e-01 4.59e+01 angle pdb=" C31 CDL A 301 " pdb=" CA7 CDL A 301 " pdb=" OA8 CDL A 301 " ideal model delta sigma weight residual 111.64 121.24 -9.60 1.65e+00 3.69e-01 3.40e+01 angle pdb=" C71 CDL A 301 " pdb=" CB7 CDL A 301 " pdb=" OB8 CDL A 301 " ideal model delta sigma weight residual 111.64 120.69 -9.05 1.65e+00 3.69e-01 3.02e+01 angle pdb=" OB6 CDL A 301 " pdb=" CB5 CDL A 301 " pdb=" OB7 CDL A 301 " ideal model delta sigma weight residual 123.92 118.79 5.13 1.00e+00 9.92e-01 2.61e+01 ... (remaining 7909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.64: 3281 24.64 - 49.29: 173 49.29 - 73.93: 26 73.93 - 98.57: 6 98.57 - 123.22: 1 Dihedral angle restraints: 3487 sinusoidal: 1359 harmonic: 2128 Sorted by residual: dihedral pdb=" CB CYS A 10 " pdb=" SG CYS A 10 " pdb=" SG CYS A 77 " pdb=" CB CYS A 77 " ideal model delta sinusoidal sigma weight residual -86.00 -121.91 35.91 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" N1 PTY B 301 " pdb=" C2 PTY B 301 " pdb=" C3 PTY B 301 " pdb=" O11 PTY B 301 " ideal model delta sinusoidal sigma weight residual 65.33 -57.89 123.22 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" CA ASP A 17 " pdb=" C ASP A 17 " pdb=" N PHE A 18 " pdb=" CA PHE A 18 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 569 0.033 - 0.066: 195 0.066 - 0.099: 59 0.099 - 0.132: 31 0.132 - 0.166: 2 Chirality restraints: 856 Sorted by residual: chirality pdb=" CB THR L 107 " pdb=" CA THR L 107 " pdb=" OG1 THR L 107 " pdb=" CG2 THR L 107 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ILE L 130 " pdb=" N ILE L 130 " pdb=" C ILE L 130 " pdb=" CB ILE L 130 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE L 72 " pdb=" N ILE L 72 " pdb=" C ILE L 72 " pdb=" CB ILE L 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 853 not shown) Planarity restraints: 1015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 87 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO A 88 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 179 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.57e+00 pdb=" CD GLN C 179 " 0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN C 179 " -0.008 2.00e-02 2.50e+03 pdb=" NE2 GLN C 179 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 145 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO B 146 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.017 5.00e-02 4.00e+02 ... (remaining 1012 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1185 2.77 - 3.30: 5377 3.30 - 3.84: 9555 3.84 - 4.37: 11568 4.37 - 4.90: 20434 Nonbonded interactions: 48119 Sorted by model distance: nonbonded pdb=" OD1 ASP L 50 " pdb=" OG SER L 55 " model vdw 2.240 2.440 nonbonded pdb=" OD1 ASP C 361 " pdb=" NH1 ARG H 72 " model vdw 2.288 2.520 nonbonded pdb=" NZ LYS L 63 " pdb=" O ASP L 105 " model vdw 2.293 2.520 nonbonded pdb=" O ASN C 286 " pdb=" OG1 THR C 290 " model vdw 2.298 2.440 nonbonded pdb=" NH2 ARG A 83 " pdb=" OD2 ASP A 87 " model vdw 2.301 2.520 ... (remaining 48114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.820 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: 7.030 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.130 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.006 0.122 5867 Z= 0.371 Angle : 0.704 9.828 7914 Z= 0.378 Chirality : 0.041 0.166 856 Planarity : 0.003 0.040 1015 Dihedral : 14.972 123.216 2126 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.31), residues: 748 helix: 1.78 (0.27), residues: 360 sheet: 0.10 (0.44), residues: 144 loop : 0.01 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 66 HIS 0.004 0.001 HIS A 33 PHE 0.008 0.001 PHE L 95 TYR 0.013 0.001 TYR H 117 ARG 0.002 0.000 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.730 Fit side-chains REVERT: C 157 LYS cc_start: 0.8722 (mptt) cc_final: 0.8488 (mptp) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 1.2513 time to fit residues: 157.0565 Evaluate side-chains 91 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.0170 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN C 286 ASN C 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5867 Z= 0.187 Angle : 0.498 5.086 7914 Z= 0.265 Chirality : 0.041 0.135 856 Planarity : 0.004 0.037 1015 Dihedral : 10.136 79.531 919 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.87 % Allowed : 10.05 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.32), residues: 748 helix: 2.28 (0.26), residues: 373 sheet: 0.11 (0.44), residues: 144 loop : 0.03 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.002 0.001 HIS H 54 PHE 0.016 0.001 PHE A 18 TYR 0.012 0.001 TYR H 117 ARG 0.004 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.642 Fit side-chains REVERT: A 89 TRP cc_start: 0.5730 (m-90) cc_final: 0.5480 (m-90) REVERT: A 131 MET cc_start: 0.8312 (tmm) cc_final: 0.7327 (mmp) REVERT: B 144 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7980 (ttm-80) REVERT: C 157 LYS cc_start: 0.8567 (mptt) cc_final: 0.8295 (mptp) REVERT: L 117 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.8004 (pt0) outliers start: 16 outliers final: 4 residues processed: 109 average time/residue: 1.1279 time to fit residues: 129.4061 Evaluate side-chains 98 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 65 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN B 173 HIS C 179 GLN C 286 ASN C 335 GLN C 392 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5867 Z= 0.248 Angle : 0.501 5.361 7914 Z= 0.264 Chirality : 0.041 0.136 856 Planarity : 0.004 0.039 1015 Dihedral : 9.532 74.599 919 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.05 % Allowed : 12.21 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.31), residues: 748 helix: 2.46 (0.26), residues: 373 sheet: 0.07 (0.43), residues: 137 loop : 0.03 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 PHE 0.010 0.001 PHE C 322 TYR 0.014 0.001 TYR H 117 ARG 0.004 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.675 Fit side-chains REVERT: A 89 TRP cc_start: 0.5774 (m-90) cc_final: 0.5493 (m-90) REVERT: A 130 LEU cc_start: 0.9219 (mt) cc_final: 0.8805 (tt) REVERT: A 131 MET cc_start: 0.8333 (tmm) cc_final: 0.7409 (mmt) REVERT: B 144 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7916 (ttm-80) REVERT: C 157 LYS cc_start: 0.8513 (mptt) cc_final: 0.8203 (mptp) REVERT: H 35 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: H 105 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8387 (mm-40) outliers start: 17 outliers final: 6 residues processed: 109 average time/residue: 1.1509 time to fit residues: 131.6739 Evaluate side-chains 100 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 0.0470 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 GLN C 286 ASN C 335 GLN C 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5867 Z= 0.201 Angle : 0.471 5.193 7914 Z= 0.247 Chirality : 0.040 0.133 856 Planarity : 0.003 0.041 1015 Dihedral : 9.057 68.622 919 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.23 % Allowed : 13.64 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.32), residues: 748 helix: 2.59 (0.26), residues: 373 sheet: 0.16 (0.43), residues: 137 loop : 0.08 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 PHE 0.010 0.001 PHE A 96 TYR 0.013 0.001 TYR H 117 ARG 0.003 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.686 Fit side-chains REVERT: A 55 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8739 (mtmt) REVERT: A 130 LEU cc_start: 0.9218 (mt) cc_final: 0.8899 (tt) REVERT: A 131 MET cc_start: 0.8304 (tmm) cc_final: 0.7409 (mmt) REVERT: B 144 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7912 (ttm-80) REVERT: C 157 LYS cc_start: 0.8513 (mptt) cc_final: 0.8221 (mptp) REVERT: H 101 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8561 (mtp) REVERT: H 105 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8424 (mm-40) outliers start: 18 outliers final: 6 residues processed: 112 average time/residue: 1.1215 time to fit residues: 131.8240 Evaluate side-chains 108 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 29 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 GLN C 286 ASN C 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5867 Z= 0.227 Angle : 0.490 5.286 7914 Z= 0.258 Chirality : 0.041 0.163 856 Planarity : 0.004 0.049 1015 Dihedral : 8.967 67.573 919 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.41 % Allowed : 15.08 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.32), residues: 748 helix: 2.60 (0.26), residues: 373 sheet: 0.20 (0.44), residues: 137 loop : 0.05 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.002 0.001 HIS H 54 PHE 0.010 0.001 PHE A 96 TYR 0.013 0.001 TYR H 117 ARG 0.003 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.653 Fit side-chains REVERT: A 131 MET cc_start: 0.8284 (tmm) cc_final: 0.7445 (mmt) REVERT: B 144 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7930 (ttm-80) REVERT: C 157 LYS cc_start: 0.8530 (mptt) cc_final: 0.8247 (mptp) REVERT: L 117 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: H 35 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: H 105 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8490 (mm-40) outliers start: 19 outliers final: 8 residues processed: 109 average time/residue: 1.1652 time to fit residues: 133.1941 Evaluate side-chains 107 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN C 179 GLN C 286 ASN C 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5867 Z= 0.227 Angle : 0.486 5.251 7914 Z= 0.256 Chirality : 0.041 0.156 856 Planarity : 0.004 0.043 1015 Dihedral : 8.954 67.867 919 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.41 % Allowed : 16.16 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.32), residues: 748 helix: 2.61 (0.26), residues: 373 sheet: 0.20 (0.43), residues: 137 loop : 0.03 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 PHE 0.010 0.001 PHE A 96 TYR 0.013 0.001 TYR H 117 ARG 0.003 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.694 Fit side-chains REVERT: A 109 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6794 (mtm-85) REVERT: A 131 MET cc_start: 0.8276 (tmm) cc_final: 0.7374 (mmp) REVERT: B 144 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7928 (ttm-80) REVERT: C 157 LYS cc_start: 0.8516 (mptt) cc_final: 0.8217 (mptp) REVERT: C 328 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8118 (tp-100) REVERT: C 331 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8450 (mp) REVERT: L 117 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: H 35 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: H 105 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8454 (mm-40) outliers start: 19 outliers final: 10 residues processed: 111 average time/residue: 1.2064 time to fit residues: 140.1386 Evaluate side-chains 114 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN C 179 GLN C 286 ASN C 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5867 Z= 0.215 Angle : 0.488 5.984 7914 Z= 0.255 Chirality : 0.040 0.140 856 Planarity : 0.003 0.043 1015 Dihedral : 8.885 68.488 919 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.05 % Allowed : 17.59 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.32), residues: 748 helix: 2.65 (0.26), residues: 373 sheet: 0.21 (0.43), residues: 137 loop : 0.03 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.002 0.001 HIS H 54 PHE 0.010 0.001 PHE A 96 TYR 0.012 0.001 TYR H 117 ARG 0.003 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.686 Fit side-chains REVERT: A 109 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6800 (mtm-85) REVERT: A 131 MET cc_start: 0.8243 (tmm) cc_final: 0.7386 (mmp) REVERT: B 144 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7915 (ttm-80) REVERT: C 157 LYS cc_start: 0.8527 (mptt) cc_final: 0.8206 (mptp) REVERT: C 328 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8090 (tp-100) REVERT: C 331 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8445 (mp) REVERT: L 117 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8071 (pt0) REVERT: H 35 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7960 (mp10) REVERT: H 105 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8441 (mm-40) outliers start: 17 outliers final: 9 residues processed: 109 average time/residue: 1.2649 time to fit residues: 144.3884 Evaluate side-chains 113 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.0980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN C 179 GLN C 286 ASN C 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5867 Z= 0.164 Angle : 0.471 7.253 7914 Z= 0.246 Chirality : 0.039 0.128 856 Planarity : 0.003 0.043 1015 Dihedral : 8.589 69.121 919 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.05 % Allowed : 17.59 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.32), residues: 748 helix: 2.74 (0.26), residues: 373 sheet: 0.31 (0.44), residues: 137 loop : 0.05 (0.44), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.002 0.001 HIS A 33 PHE 0.010 0.001 PHE A 96 TYR 0.011 0.001 TYR H 117 ARG 0.003 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.655 Fit side-chains REVERT: A 109 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6790 (mtm-85) REVERT: A 131 MET cc_start: 0.8211 (tmm) cc_final: 0.7384 (mmp) REVERT: B 144 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7896 (ttm-80) REVERT: C 157 LYS cc_start: 0.8500 (mptt) cc_final: 0.8184 (mptp) REVERT: C 328 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8105 (tp-100) REVERT: C 331 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8390 (mp) REVERT: H 105 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8453 (mm-40) outliers start: 17 outliers final: 6 residues processed: 112 average time/residue: 1.1799 time to fit residues: 138.8467 Evaluate side-chains 107 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 42 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 GLN C 286 ASN C 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5867 Z= 0.203 Angle : 0.493 7.362 7914 Z= 0.256 Chirality : 0.040 0.129 856 Planarity : 0.003 0.043 1015 Dihedral : 8.626 68.652 919 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.51 % Allowed : 18.67 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.32), residues: 748 helix: 2.69 (0.26), residues: 374 sheet: 0.29 (0.44), residues: 137 loop : 0.04 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.002 0.001 HIS A 33 PHE 0.010 0.001 PHE A 96 TYR 0.012 0.001 TYR H 117 ARG 0.002 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.687 Fit side-chains REVERT: A 109 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6797 (mtm-85) REVERT: A 131 MET cc_start: 0.8222 (tmm) cc_final: 0.7413 (mmp) REVERT: C 157 LYS cc_start: 0.8512 (mptt) cc_final: 0.8198 (mptp) REVERT: C 328 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8109 (tp-100) REVERT: C 331 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8429 (mp) REVERT: H 105 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8449 (mm-40) outliers start: 14 outliers final: 8 residues processed: 106 average time/residue: 1.1685 time to fit residues: 129.9077 Evaluate side-chains 109 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 286 ASN C 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5867 Z= 0.221 Angle : 0.503 8.061 7914 Z= 0.260 Chirality : 0.041 0.134 856 Planarity : 0.003 0.043 1015 Dihedral : 8.709 68.467 919 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.33 % Allowed : 18.85 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.32), residues: 748 helix: 2.67 (0.26), residues: 374 sheet: 0.26 (0.44), residues: 137 loop : 0.04 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.002 0.001 HIS H 54 PHE 0.010 0.001 PHE A 96 TYR 0.012 0.001 TYR H 117 ARG 0.002 0.000 ARG L 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.731 Fit side-chains REVERT: A 109 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6819 (mtm-85) REVERT: A 131 MET cc_start: 0.8179 (tmm) cc_final: 0.7379 (mmp) REVERT: C 157 LYS cc_start: 0.8519 (mptt) cc_final: 0.8245 (mptp) REVERT: C 328 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8110 (tp-100) REVERT: C 331 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8436 (mp) REVERT: H 105 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8437 (mm-40) outliers start: 13 outliers final: 8 residues processed: 106 average time/residue: 1.2571 time to fit residues: 139.4285 Evaluate side-chains 109 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 0.0170 chunk 42 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 GLN C 286 ASN C 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.081447 restraints weight = 8807.490| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.13 r_work: 0.2877 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5867 Z= 0.205 Angle : 0.501 8.007 7914 Z= 0.258 Chirality : 0.040 0.130 856 Planarity : 0.003 0.043 1015 Dihedral : 8.675 68.364 919 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.87 % Allowed : 18.85 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.32), residues: 748 helix: 2.67 (0.26), residues: 374 sheet: 0.26 (0.44), residues: 137 loop : 0.02 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.002 0.001 HIS A 33 PHE 0.010 0.001 PHE A 96 TYR 0.012 0.001 TYR H 117 ARG 0.002 0.000 ARG L 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2837.72 seconds wall clock time: 51 minutes 37.76 seconds (3097.76 seconds total)