Starting phenix.real_space_refine on Fri Dec 27 19:17:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8scx_40346/12_2024/8scx_40346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8scx_40346/12_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/cci-nas-00/data/ceres_data/8scx_40346/12_2024/8scx_40346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8scx_40346/12_2024/8scx_40346.map" model { file = "/net/cci-nas-00/data/ceres_data/8scx_40346/12_2024/8scx_40346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8scx_40346/12_2024/8scx_40346.cif" } 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. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.59, per 1000 atoms: 0.80 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 - 3.00 Amino acid : True - 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: 1.53 Conformation dependent library (CDL) restraints added in 892.6 milliseconds 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... Secondary structure from input PDB file: 23 helices and 8 sheets defined 53.6% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 9 through 41 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 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 84 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 89 through 103 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 107 through 138 Processing helix chain 'B' and resid 92 through 122 removed outlier: 3.755A pdb=" N ASP B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 171 Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 174 through 190 Processing helix chain 'B' and resid 195 through 220 removed outlier: 3.936A pdb=" N GLY B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) 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 126 Processing helix chain 'C' and resid 126 through 152 Proline residue: C 149 - end of helix Processing helix chain 'C' and resid 153 through 164 removed outlier: 3.586A pdb=" N LYS C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 172 removed outlier: 3.730A pdb=" N SER C 169 " --> pdb=" O GLY C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 Processing helix chain 'C' and resid 256 through 266 removed outlier: 3.554A pdb=" N PHE C 265 " --> pdb=" O VAL C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 285 through 296 Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 309 through 317 removed outlier: 3.758A pdb=" N LYS C 315 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 335 removed outlier: 3.614A pdb=" N GLU C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.504A pdb=" N THR H 109 " --> pdb=" O ALA H 106 " (cutoff:3.500A) 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=AA1, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.246A pdb=" N ILE C 362 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS C 355 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL C 364 " --> pdb=" O SER C 353 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N SER C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 366 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE C 351 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY C 368 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL C 349 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP C 345 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE C 374 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE C 343 " --> pdb=" O ILE C 374 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 337 through 339 removed outlier: 5.110A pdb=" N ARG C 404 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN C 375 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN C 392 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N TYR C 377 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N GLU C 390 " --> pdb=" O TYR C 377 " (cutoff:3.500A) removed outlier: 10.715A pdb=" N LYS C 379 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 12.824A pdb=" N GLY C 388 " --> pdb=" O LYS C 379 " (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=AA3, 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=AA4, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.922A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N MET L 57 " --> pdb=" O TYR L 73 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR L 73 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'H' and resid 22 through 26 Processing sheet with id=AA7, first strand: chain 'H' and resid 76 through 78 removed outlier: 6.814A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL H 69 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY H 52 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE H 111 " --> pdb=" O GLN H 58 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR H 125 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 76 through 78 removed outlier: 6.814A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL H 69 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY H 52 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE H 111 " --> pdb=" O GLN H 58 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1146 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: 1.68 Time building geometry restraints manager: 1.77 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: 0.00 - 1.97: 7731 1.97 - 3.93: 139 3.93 - 5.90: 33 5.90 - 7.86: 3 7.86 - 9.83: 8 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: 1171 2.77 - 3.30: 5340 3.30 - 3.84: 9508 3.84 - 4.37: 11499 4.37 - 4.90: 20429 Nonbonded interactions: 47947 Sorted by model distance: nonbonded pdb=" OD1 ASP L 50 " pdb=" OG SER L 55 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP C 361 " pdb=" NH1 ARG H 72 " model vdw 2.288 3.120 nonbonded pdb=" NZ LYS L 63 " pdb=" O ASP L 105 " model vdw 2.293 3.120 nonbonded pdb=" O ASN C 286 " pdb=" OG1 THR C 290 " model vdw 2.298 3.040 nonbonded pdb=" NH2 ARG A 83 " pdb=" OD2 ASP A 87 " model vdw 2.301 3.120 ... (remaining 47942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.390 Find NCS groups from input model: 0.070 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:13.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.130 ------------------------------------------------------------------------------- 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= 0.380 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 to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.547 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: 1.3908 time to fit residues: 174.2242 Evaluate side-chains 91 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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: 1.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 392 ASN L 62 GLN H 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5867 Z= 0.288 Angle : 0.549 5.496 7914 Z= 0.292 Chirality : 0.043 0.135 856 Planarity : 0.004 0.044 1015 Dihedral : 10.291 78.911 919 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.33 % Allowed : 10.59 % 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: 1.86 (0.31), residues: 748 helix: 2.47 (0.25), residues: 375 sheet: 0.13 (0.44), residues: 144 loop : -0.06 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.004 0.001 HIS H 54 PHE 0.015 0.001 PHE A 18 TYR 0.014 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 114 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.694 Fit side-chains REVERT: A 131 MET cc_start: 0.8335 (tmm) cc_final: 0.7273 (mmp) REVERT: C 157 LYS cc_start: 0.8669 (mptt) cc_final: 0.8322 (mptp) REVERT: H 35 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8125 (mp10) outliers start: 13 outliers final: 4 residues processed: 106 average time/residue: 1.2321 time to fit residues: 136.5523 Evaluate side-chains 98 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain H residue 35 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5867 Z= 0.252 Angle : 0.512 5.219 7914 Z= 0.272 Chirality : 0.041 0.133 856 Planarity : 0.004 0.040 1015 Dihedral : 9.593 72.648 919 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.05 % Allowed : 13.82 % 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: 2.11 (0.31), residues: 748 helix: 2.79 (0.26), residues: 377 sheet: 0.15 (0.43), residues: 144 loop : -0.11 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.004 0.001 HIS H 54 PHE 0.011 0.001 PHE C 322 TYR 0.013 0.001 TYR H 117 ARG 0.003 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 118 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.501 Fit side-chains REVERT: A 109 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6818 (mtm-85) REVERT: A 131 MET cc_start: 0.8286 (tmm) cc_final: 0.7335 (mmp) REVERT: B 144 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7171 (tpm-80) REVERT: C 157 LYS cc_start: 0.8650 (mptt) cc_final: 0.8301 (mptp) REVERT: L 117 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.8031 (pt0) REVERT: H 35 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8128 (mp10) REVERT: H 91 ASP cc_start: 0.7971 (t70) cc_final: 0.7730 (t70) outliers start: 17 outliers final: 5 residues processed: 107 average time/residue: 1.4247 time to fit residues: 158.7446 Evaluate side-chains 101 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 35 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 0.0010 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.0070 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 chunk 71 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5867 Z= 0.168 Angle : 0.479 5.039 7914 Z= 0.255 Chirality : 0.040 0.130 856 Planarity : 0.004 0.041 1015 Dihedral : 9.061 69.094 919 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.59 % Allowed : 14.36 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.32), residues: 748 helix: 2.97 (0.26), residues: 377 sheet: 0.28 (0.43), residues: 144 loop : -0.03 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS A 33 PHE 0.012 0.001 PHE A 18 TYR 0.011 0.001 TYR H 117 ARG 0.004 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 127 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.649 Fit side-chains REVERT: A 109 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6836 (mtm-85) REVERT: A 131 MET cc_start: 0.8260 (tmm) cc_final: 0.7343 (mmp) REVERT: B 144 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7290 (tpm-80) REVERT: C 157 LYS cc_start: 0.8663 (mptt) cc_final: 0.8286 (mptp) REVERT: L 117 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: H 91 ASP cc_start: 0.7909 (t70) cc_final: 0.7642 (t70) outliers start: 20 outliers final: 6 residues processed: 115 average time/residue: 1.3292 time to fit residues: 159.3540 Evaluate side-chains 110 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 30 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 0.0770 chunk 29 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 36 optimal weight: 0.0770 chunk 64 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN C 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5867 Z= 0.170 Angle : 0.491 6.082 7914 Z= 0.260 Chirality : 0.041 0.169 856 Planarity : 0.004 0.053 1015 Dihedral : 8.830 67.474 919 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.87 % Allowed : 16.34 % Favored : 80.79 % 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: 2.35 (0.31), residues: 748 helix: 2.97 (0.26), residues: 377 sheet: 0.37 (0.43), residues: 144 loop : -0.07 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.003 0.001 HIS A 33 PHE 0.011 0.001 PHE A 18 TYR 0.011 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 118 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.728 Fit side-chains REVERT: A 109 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6835 (mtm-85) REVERT: A 131 MET cc_start: 0.8270 (tmm) cc_final: 0.7379 (mmp) REVERT: B 144 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7320 (tpm-80) REVERT: C 157 LYS cc_start: 0.8604 (mptt) cc_final: 0.8200 (mptp) REVERT: C 331 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8376 (mp) REVERT: H 91 ASP cc_start: 0.7863 (t70) cc_final: 0.7591 (t70) outliers start: 16 outliers final: 4 residues processed: 109 average time/residue: 1.3780 time to fit residues: 156.7356 Evaluate side-chains 106 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain L residue 33 VAL 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: 0.2980 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.0030 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN C 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5867 Z= 0.220 Angle : 0.500 5.885 7914 Z= 0.263 Chirality : 0.041 0.164 856 Planarity : 0.004 0.049 1015 Dihedral : 8.996 67.488 919 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.33 % Allowed : 17.41 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.31), residues: 748 helix: 3.00 (0.25), residues: 377 sheet: 0.39 (0.43), residues: 144 loop : -0.06 (0.43), residues: 227 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 0.012 0.001 TYR H 117 ARG 0.002 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 117 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.687 Fit side-chains REVERT: A 131 MET cc_start: 0.8258 (tmm) cc_final: 0.7386 (mmp) REVERT: B 144 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7311 (tpm-80) REVERT: C 157 LYS cc_start: 0.8610 (mptt) cc_final: 0.8238 (mptp) REVERT: C 331 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8366 (mp) REVERT: L 117 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: H 35 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8111 (mp10) REVERT: H 91 ASP cc_start: 0.7865 (t70) cc_final: 0.7596 (t70) outliers start: 13 outliers final: 6 residues processed: 109 average time/residue: 1.2196 time to fit residues: 139.2294 Evaluate side-chains 108 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 123 ASN 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 L residue 33 VAL Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 65 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 0.0050 chunk 44 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN C 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5867 Z= 0.215 Angle : 0.513 6.975 7914 Z= 0.269 Chirality : 0.041 0.149 856 Planarity : 0.004 0.048 1015 Dihedral : 8.992 67.810 919 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.05 % Allowed : 17.95 % Favored : 78.99 % 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: 2.45 (0.31), residues: 748 helix: 3.06 (0.25), residues: 377 sheet: 0.48 (0.43), residues: 137 loop : -0.07 (0.42), residues: 234 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 0.012 0.001 TYR H 117 ARG 0.001 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 119 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.812 Fit side-chains REVERT: A 131 MET cc_start: 0.8252 (tmm) cc_final: 0.7383 (mmp) REVERT: B 144 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7303 (tpm-80) REVERT: C 157 LYS cc_start: 0.8611 (mptt) cc_final: 0.8337 (mptp) REVERT: C 331 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8367 (mp) REVERT: L 117 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8057 (pt0) REVERT: H 35 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: H 91 ASP cc_start: 0.7856 (t70) cc_final: 0.7584 (t70) outliers start: 17 outliers final: 8 residues processed: 110 average time/residue: 1.3260 time to fit residues: 152.1918 Evaluate side-chains 109 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 65 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.2980 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 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: 0.9980 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5867 Z= 0.222 Angle : 0.510 7.340 7914 Z= 0.268 Chirality : 0.041 0.145 856 Planarity : 0.004 0.048 1015 Dihedral : 8.910 67.983 919 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.05 % Allowed : 17.77 % Favored : 79.17 % 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: 2.49 (0.31), residues: 748 helix: 3.07 (0.25), residues: 378 sheet: 0.50 (0.43), residues: 137 loop : -0.02 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 PHE 0.010 0.001 PHE A 96 TYR 0.012 0.001 TYR H 117 ARG 0.001 0.000 ARG A 109 *********************** 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 116 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.648 Fit side-chains REVERT: A 131 MET cc_start: 0.8265 (tmm) cc_final: 0.7423 (mmp) REVERT: B 144 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7298 (tpm-80) REVERT: C 157 LYS cc_start: 0.8610 (mptt) cc_final: 0.8333 (mptp) REVERT: C 331 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8370 (mp) REVERT: L 117 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: H 35 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8085 (mp10) REVERT: H 91 ASP cc_start: 0.7846 (t70) cc_final: 0.7572 (t70) outliers start: 17 outliers final: 7 residues processed: 107 average time/residue: 1.3657 time to fit residues: 152.4970 Evaluate side-chains 106 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 123 ASN 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 335 GLN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 65 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 30.0000 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2299 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= 0.264 Angle : 0.546 7.917 7914 Z= 0.286 Chirality : 0.042 0.153 856 Planarity : 0.004 0.048 1015 Dihedral : 8.980 68.012 919 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: 2.43 (0.31), residues: 748 helix: 3.00 (0.25), residues: 379 sheet: 0.48 (0.43), residues: 137 loop : -0.03 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.004 0.001 HIS H 54 PHE 0.010 0.001 PHE A 96 TYR 0.013 0.001 TYR H 117 ARG 0.002 0.000 ARG H 116 *********************** 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 112 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.693 Fit side-chains REVERT: A 131 MET cc_start: 0.8266 (tmm) cc_final: 0.7429 (mmp) REVERT: B 144 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7286 (tpm-80) REVERT: C 157 LYS cc_start: 0.8613 (mptt) cc_final: 0.8335 (mptp) REVERT: C 331 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8395 (mp) REVERT: L 117 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8081 (pt0) REVERT: H 35 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8091 (mp10) REVERT: H 91 ASP cc_start: 0.7860 (t70) cc_final: 0.7595 (t70) REVERT: H 101 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8548 (mtp) outliers start: 14 outliers final: 6 residues processed: 103 average time/residue: 1.3092 time to fit residues: 140.9025 Evaluate side-chains 107 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 123 ASN 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 L residue 33 VAL 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 101 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5867 Z= 0.215 Angle : 0.523 8.461 7914 Z= 0.274 Chirality : 0.041 0.145 856 Planarity : 0.004 0.048 1015 Dihedral : 8.822 68.311 919 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.97 % Allowed : 19.57 % Favored : 78.46 % 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: 2.47 (0.31), residues: 748 helix: 3.04 (0.25), residues: 379 sheet: 0.49 (0.43), residues: 137 loop : -0.02 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 PHE 0.010 0.001 PHE A 96 TYR 0.012 0.001 TYR H 117 ARG 0.001 0.000 ARG A 109 ********************** 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 109 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.603 Fit side-chains REVERT: A 131 MET cc_start: 0.8215 (tmm) cc_final: 0.7438 (mmp) REVERT: B 144 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7289 (tpm-80) REVERT: B 184 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8583 (tt) REVERT: C 157 LYS cc_start: 0.8608 (mptt) cc_final: 0.8219 (mptp) REVERT: C 331 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8384 (mp) REVERT: L 117 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8069 (pt0) REVERT: H 35 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: H 91 ASP cc_start: 0.7833 (t70) cc_final: 0.7540 (t70) REVERT: H 101 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8522 (mtp) outliers start: 11 outliers final: 5 residues processed: 103 average time/residue: 1.2360 time to fit residues: 133.2798 Evaluate side-chains 108 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain L residue 33 VAL 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 101 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.080890 restraints weight = 8735.442| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.13 r_work: 0.2866 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5867 Z= 0.213 Angle : 0.533 8.409 7914 Z= 0.278 Chirality : 0.041 0.145 856 Planarity : 0.004 0.048 1015 Dihedral : 8.732 68.373 919 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.97 % Allowed : 19.57 % Favored : 78.46 % 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: 2.51 (0.31), residues: 748 helix: 3.06 (0.25), residues: 379 sheet: 0.54 (0.43), residues: 137 loop : -0.01 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 66 HIS 0.003 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2919.29 seconds wall clock time: 53 minutes 7.11 seconds (3187.11 seconds total)