Starting phenix.real_space_refine on Thu Jul 2 03:56:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8scx_40346/07_2026/8scx_40346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8scx_40346/07_2026/8scx_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 { model { file = "/net/cci-nas-00/data/ceres_data/8scx_40346/07_2026/8scx_40346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8scx_40346/07_2026/8scx_40346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8scx_40346/07_2026/8scx_40346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8scx_40346/07_2026/8scx_40346.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8scx_40346/07_2026/8scx_40346.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8scx_40346/07_2026/8scx_40346.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'GLU:plan': 10, 'HIS:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} 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: 1.13, per 1000 atoms: 0.20 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: 0.46 Conformation dependent library (CDL) restraints added in 231.1 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: 0.17 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: 1.01 Time building geometry restraints manager: 0.61 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: 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: 3270 24.64 - 49.29: 164 49.29 - 73.93: 23 73.93 - 98.57: 3 98.57 - 123.22: 1 Dihedral angle restraints: 3461 sinusoidal: 1333 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 3458 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: 2.480 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: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.270 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 5870 Z= 0.334 Angle : 0.710 9.828 7920 Z= 0.380 Chirality : 0.041 0.166 856 Planarity : 0.003 0.040 1015 Dihedral : 14.401 123.216 2100 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.65 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG H 116 TYR 0.013 0.001 TYR H 117 PHE 0.008 0.001 PHE L 95 TRP 0.014 0.001 TRP H 66 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.33 ( 5867) covalent geometry : angle 0.70440 / 0.38 ( 7914) SS BOND : bond 0.00258 / 0.13 ( 3) SS BOND : angle 3.34137 / 1.78 ( 6) hydrogen bonds : bond 0.21156 / 14.24 ( 384) hydrogen bonds : angle 7.61792 / 5.62 ( 1146) *********************** 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 : 0.241 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: 0.5907 time to fit residues: 73.9268 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 : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 133 GLN B 163 ASN B 173 HIS C 179 GLN C 286 ASN C 392 ASN L 62 GLN H 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.079474 restraints weight = 8996.396| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.13 r_work: 0.2838 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5870 Z= 0.189 Angle : 0.550 5.337 7920 Z= 0.295 Chirality : 0.042 0.138 856 Planarity : 0.004 0.044 1015 Dihedral : 8.609 67.828 893 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.05 % Allowed : 9.69 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.31), residues: 748 helix: 2.52 (0.26), residues: 375 sheet: 0.14 (0.44), residues: 144 loop : -0.06 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 44 TYR 0.014 0.001 TYR H 117 PHE 0.014 0.001 PHE A 18 TRP 0.012 0.001 TRP H 66 HIS 0.004 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 5867) covalent geometry : angle 0.54771 / 0.29 ( 7914) SS BOND : bond 0.00317 / 0.16 ( 3) SS BOND : angle 1.99007 / 1.04 ( 6) hydrogen bonds : bond 0.04750 / 3.29 ( 384) hydrogen bonds : angle 4.68803 / 3.52 ( 1146) *********************** 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 115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.233 Fit side-chains REVERT: A 131 MET cc_start: 0.8148 (tmm) cc_final: 0.7090 (mmp) REVERT: B 133 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8103 (mt0) REVERT: B 144 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8372 (ttm-80) REVERT: C 157 LYS cc_start: 0.8539 (mptt) cc_final: 0.8247 (mptp) REVERT: H 35 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8249 (mp10) REVERT: H 91 ASP cc_start: 0.8015 (t70) cc_final: 0.7585 (t70) REVERT: H 105 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7961 (mm-40) outliers start: 17 outliers final: 5 residues processed: 107 average time/residue: 0.5828 time to fit residues: 65.1519 Evaluate side-chains 102 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain H residue 35 GLN 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 51 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 HIS 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 = 0.3462 r_free = 0.3462 target = 0.111465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.081287 restraints weight = 8921.176| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.13 r_work: 0.2879 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5870 Z= 0.137 Angle : 0.497 5.103 7920 Z= 0.264 Chirality : 0.041 0.133 856 Planarity : 0.004 0.039 1015 Dihedral : 7.358 58.531 893 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.87 % Allowed : 12.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.32), residues: 748 helix: 2.80 (0.26), residues: 377 sheet: 0.22 (0.44), residues: 144 loop : -0.06 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 44 TYR 0.012 0.001 TYR H 117 PHE 0.011 0.001 PHE A 18 TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 5867) covalent geometry : angle 0.49629 / 0.26 ( 7914) SS BOND : bond 0.00261 / 0.13 ( 3) SS BOND : angle 1.23352 / 0.64 ( 6) hydrogen bonds : bond 0.03814 / 2.68 ( 384) hydrogen bonds : angle 4.18170 / 3.17 ( 1146) *********************** 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 to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.317 Fit side-chains REVERT: A 86 GLU cc_start: 0.8321 (tt0) cc_final: 0.7568 (tm-30) REVERT: A 131 MET cc_start: 0.8028 (tmm) cc_final: 0.7079 (mmp) REVERT: B 133 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7899 (mm-40) REVERT: B 144 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8337 (ttm-80) REVERT: C 157 LYS cc_start: 0.8507 (mptt) cc_final: 0.8148 (mptp) REVERT: L 117 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8577 (pt0) REVERT: H 91 ASP cc_start: 0.7965 (t70) cc_final: 0.7379 (t70) REVERT: H 105 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7929 (mm-40) outliers start: 16 outliers final: 4 residues processed: 112 average time/residue: 0.6004 time to fit residues: 70.2757 Evaluate side-chains 104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 144 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 ASN B 160 ASN C 286 ASN C 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.079696 restraints weight = 8995.225| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.14 r_work: 0.2853 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5870 Z= 0.177 Angle : 0.506 5.321 7920 Z= 0.268 Chirality : 0.042 0.132 856 Planarity : 0.004 0.041 1015 Dihedral : 7.304 57.725 893 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.41 % Allowed : 14.36 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.31), residues: 748 helix: 2.91 (0.26), residues: 377 sheet: 0.21 (0.43), residues: 144 loop : -0.04 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 44 TYR 0.013 0.001 TYR H 117 PHE 0.011 0.001 PHE C 322 TRP 0.012 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 5867) covalent geometry : angle 0.50496 / 0.27 ( 7914) SS BOND : bond 0.00350 / 0.17 ( 3) SS BOND : angle 1.01821 / 0.52 ( 6) hydrogen bonds : bond 0.03786 / 2.65 ( 384) hydrogen bonds : angle 4.08932 / 3.09 ( 1146) *********************** 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 117 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.239 Fit side-chains REVERT: A 86 GLU cc_start: 0.8276 (tt0) cc_final: 0.7524 (tm-30) REVERT: A 109 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7043 (mtm-85) REVERT: A 131 MET cc_start: 0.8052 (tmm) cc_final: 0.7132 (mmp) REVERT: B 144 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8318 (ttm-80) REVERT: C 157 LYS cc_start: 0.8515 (mptt) cc_final: 0.8171 (mptp) REVERT: H 35 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: H 91 ASP cc_start: 0.8044 (t70) cc_final: 0.7396 (t70) REVERT: H 105 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7926 (mm-40) outliers start: 19 outliers final: 4 residues processed: 107 average time/residue: 0.6067 time to fit residues: 67.7184 Evaluate side-chains 101 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 L residue 33 VAL Chi-restraints excluded: chain H residue 35 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 ASN 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 = 0.3451 r_free = 0.3451 target = 0.110828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.080028 restraints weight = 9020.291| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.17 r_work: 0.2857 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5870 Z= 0.168 Angle : 0.519 7.422 7920 Z= 0.275 Chirality : 0.042 0.191 856 Planarity : 0.004 0.050 1015 Dihedral : 7.286 56.227 893 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.05 % Allowed : 16.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.31), residues: 748 helix: 2.87 (0.26), residues: 377 sheet: 0.25 (0.43), residues: 144 loop : -0.07 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 44 TYR 0.013 0.001 TYR H 117 PHE 0.011 0.001 PHE C 322 TRP 0.013 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 5867) covalent geometry : angle 0.51195 / 0.27 ( 7914) SS BOND : bond 0.00303 / 0.15 ( 3) SS BOND : angle 3.13789 / 1.65 ( 6) hydrogen bonds : bond 0.03701 / 2.60 ( 384) hydrogen bonds : angle 4.04440 / 3.08 ( 1146) *********************** 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: 17 poor density : 101 time to evaluate : 0.255 Fit side-chains REVERT: A 86 GLU cc_start: 0.8259 (tt0) cc_final: 0.7527 (tm-30) REVERT: A 109 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7078 (mtm-85) REVERT: A 131 MET cc_start: 0.8057 (tmm) cc_final: 0.7140 (mmp) REVERT: B 144 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8340 (ttm-80) REVERT: C 157 LYS cc_start: 0.8508 (mptt) cc_final: 0.8150 (mptp) REVERT: H 35 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: H 91 ASP cc_start: 0.8032 (t70) cc_final: 0.7471 (t70) outliers start: 17 outliers final: 5 residues processed: 109 average time/residue: 0.5656 time to fit residues: 64.4558 Evaluate side-chains 103 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 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 L residue 33 VAL Chi-restraints excluded: chain H residue 35 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN C 179 GLN C 286 ASN C 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.110280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.079674 restraints weight = 8929.466| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.14 r_work: 0.2846 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5870 Z= 0.182 Angle : 0.521 5.900 7920 Z= 0.275 Chirality : 0.042 0.170 856 Planarity : 0.004 0.047 1015 Dihedral : 7.405 56.127 893 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.69 % Allowed : 17.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.31), residues: 748 helix: 2.88 (0.26), residues: 377 sheet: 0.27 (0.43), residues: 144 loop : -0.06 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 144 TYR 0.013 0.001 TYR H 117 PHE 0.011 0.001 PHE C 322 TRP 0.014 0.001 TRP H 66 HIS 0.004 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 5867) covalent geometry : angle 0.51694 / 0.27 ( 7914) SS BOND : bond 0.00349 / 0.17 ( 3) SS BOND : angle 2.47790 / 1.30 ( 6) hydrogen bonds : bond 0.03652 / 2.56 ( 384) hydrogen bonds : angle 4.02244 / 3.05 ( 1146) *********************** 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 116 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.223 Fit side-chains REVERT: A 86 GLU cc_start: 0.8287 (tt0) cc_final: 0.7539 (tm-30) REVERT: A 131 MET cc_start: 0.8053 (tmm) cc_final: 0.7151 (mmp) REVERT: B 144 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8373 (ttm-80) REVERT: C 157 LYS cc_start: 0.8482 (mptt) cc_final: 0.8153 (mptp) REVERT: C 331 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8169 (mp) REVERT: H 35 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8209 (mp10) REVERT: H 91 ASP cc_start: 0.8024 (t70) cc_final: 0.7350 (t70) REVERT: H 101 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8778 (mtp) outliers start: 15 outliers final: 7 residues processed: 106 average time/residue: 0.5833 time to fit residues: 64.4307 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 : 0.207 ------------------------------------------------------------------------------- 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 C residue 331 ILE Chi-restraints excluded: chain L residue 33 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 ASN C 179 GLN C 286 ASN C 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.109386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.078506 restraints weight = 8998.322| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.15 r_work: 0.2830 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5870 Z= 0.223 Angle : 0.553 6.607 7920 Z= 0.291 Chirality : 0.043 0.170 856 Planarity : 0.004 0.048 1015 Dihedral : 7.701 58.511 893 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.31), residues: 748 helix: 2.85 (0.26), residues: 378 sheet: 0.30 (0.43), residues: 137 loop : -0.10 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 144 TYR 0.014 0.002 TYR H 117 PHE 0.012 0.001 PHE C 322 TRP 0.016 0.001 TRP H 66 HIS 0.004 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 ( 5867) covalent geometry : angle 0.54972 / 0.29 ( 7914) SS BOND : bond 0.00414 / 0.20 ( 3) SS BOND : angle 2.25370 / 1.18 ( 6) hydrogen bonds : bond 0.03836 / 2.68 ( 384) hydrogen bonds : angle 4.05739 / 3.08 ( 1146) *********************** 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 115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.224 Fit side-chains REVERT: A 86 GLU cc_start: 0.8273 (tt0) cc_final: 0.7544 (tm-30) REVERT: A 131 MET cc_start: 0.8060 (tmm) cc_final: 0.7151 (mmp) REVERT: B 144 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8353 (ttm-80) REVERT: C 157 LYS cc_start: 0.8473 (mptt) cc_final: 0.8106 (mptp) REVERT: H 35 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: H 91 ASP cc_start: 0.8018 (t70) cc_final: 0.7403 (t70) REVERT: H 101 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8822 (mtp) outliers start: 17 outliers final: 6 residues processed: 107 average time/residue: 0.5886 time to fit residues: 65.6998 Evaluate side-chains 103 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 L residue 33 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN C 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.110425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.080123 restraints weight = 8856.486| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.13 r_work: 0.2847 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5870 Z= 0.152 Angle : 0.512 7.268 7920 Z= 0.271 Chirality : 0.042 0.145 856 Planarity : 0.004 0.048 1015 Dihedral : 7.347 59.477 893 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.33 % Allowed : 18.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.31), residues: 748 helix: 2.93 (0.26), residues: 379 sheet: 0.29 (0.43), residues: 144 loop : -0.03 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.012 0.001 TYR H 117 PHE 0.010 0.001 PHE C 322 TRP 0.014 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 5867) covalent geometry : angle 0.51045 / 0.27 ( 7914) SS BOND : bond 0.00296 / 0.14 ( 3) SS BOND : angle 1.72125 / 0.90 ( 6) hydrogen bonds : bond 0.03457 / 2.43 ( 384) hydrogen bonds : angle 3.95752 / 3.01 ( 1146) *********************** 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 113 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.230 Fit side-chains REVERT: A 86 GLU cc_start: 0.8314 (tt0) cc_final: 0.7528 (tm-30) REVERT: A 131 MET cc_start: 0.8015 (tmm) cc_final: 0.7143 (mmp) REVERT: B 144 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8237 (ttm-80) REVERT: C 157 LYS cc_start: 0.8442 (mptt) cc_final: 0.8078 (mptp) REVERT: C 331 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8089 (mp) REVERT: H 35 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8129 (mp10) REVERT: H 91 ASP cc_start: 0.7904 (t70) cc_final: 0.7177 (t70) REVERT: H 105 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7894 (mm-40) outliers start: 13 outliers final: 7 residues processed: 107 average time/residue: 0.5875 time to fit residues: 65.5353 Evaluate side-chains 106 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 C residue 331 ILE Chi-restraints excluded: chain L residue 33 VAL 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 21 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 0.0030 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN C 179 GLN C 286 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.080606 restraints weight = 8885.929| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.13 r_work: 0.2857 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5870 Z= 0.140 Angle : 0.507 7.972 7920 Z= 0.267 Chirality : 0.041 0.147 856 Planarity : 0.004 0.048 1015 Dihedral : 7.204 59.058 893 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.56 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.31), residues: 748 helix: 2.97 (0.25), residues: 379 sheet: 0.37 (0.43), residues: 144 loop : -0.02 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 378 TYR 0.011 0.001 TYR H 117 PHE 0.010 0.001 PHE C 322 TRP 0.013 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5867) covalent geometry : angle 0.50480 / 0.27 ( 7914) SS BOND : bond 0.00264 / 0.13 ( 3) SS BOND : angle 1.63013 / 0.85 ( 6) hydrogen bonds : bond 0.03383 / 2.38 ( 384) hydrogen bonds : angle 3.89597 / 2.96 ( 1146) *********************** 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 109 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.212 Fit side-chains REVERT: A 86 GLU cc_start: 0.8358 (tt0) cc_final: 0.7594 (tm-30) REVERT: A 131 MET cc_start: 0.8045 (tmm) cc_final: 0.7171 (mmp) REVERT: B 133 GLN cc_start: 0.8409 (mt0) cc_final: 0.8121 (mt0) REVERT: B 144 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8286 (ttm-80) REVERT: C 157 LYS cc_start: 0.8468 (mptt) cc_final: 0.8089 (mptp) REVERT: C 331 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8166 (mp) REVERT: H 91 ASP cc_start: 0.7988 (t70) cc_final: 0.7321 (t70) REVERT: H 105 GLN cc_start: 0.8248 (mm-40) cc_final: 0.8008 (mm-40) outliers start: 11 outliers final: 8 residues processed: 104 average time/residue: 0.6141 time to fit residues: 66.5404 Evaluate side-chains 107 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 C residue 331 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 65 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 50 optimal weight: 0.0570 chunk 73 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 ASN C 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.081019 restraints weight = 8874.004| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.14 r_work: 0.2877 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 0.044 5870 Z= 0.131 Angle : 0.509 8.475 7920 Z= 0.267 Chirality : 0.041 0.145 856 Planarity : 0.004 0.048 1015 Dihedral : 7.055 58.837 893 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.80 % Allowed : 19.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.31), residues: 748 helix: 2.98 (0.25), residues: 379 sheet: 0.40 (0.43), residues: 144 loop : -0.00 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.011 0.001 TYR H 117 PHE 0.010 0.001 PHE A 18 TRP 0.013 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 5867) covalent geometry : angle 0.50715 / 0.27 ( 7914) SS BOND : bond 0.00249 / 0.12 ( 3) SS BOND : angle 1.57702 / 0.83 ( 6) hydrogen bonds : bond 0.03288 / 2.32 ( 384) hydrogen bonds : angle 3.86131 / 2.93 ( 1146) ********************** 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 110 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.245 Fit side-chains REVERT: A 86 GLU cc_start: 0.8323 (tt0) cc_final: 0.7589 (tm-30) REVERT: A 131 MET cc_start: 0.7987 (tmm) cc_final: 0.7166 (mmp) REVERT: B 133 GLN cc_start: 0.8353 (mt0) cc_final: 0.8060 (mt0) REVERT: B 144 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8242 (ttm-80) REVERT: C 157 LYS cc_start: 0.8446 (mptt) cc_final: 0.8080 (mptp) REVERT: C 331 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8135 (mp) REVERT: H 91 ASP cc_start: 0.7912 (t70) cc_final: 0.7183 (t70) REVERT: H 105 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7927 (mm-40) outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.5670 time to fit residues: 62.1052 Evaluate side-chains 107 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 331 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain H residue 65 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 ASN C 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.079150 restraints weight = 8832.038| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.12 r_work: 0.2843 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5870 Z= 0.198 Angle : 0.545 8.411 7920 Z= 0.286 Chirality : 0.043 0.157 856 Planarity : 0.004 0.048 1015 Dihedral : 7.379 57.627 893 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.31), residues: 748 helix: 2.94 (0.25), residues: 379 sheet: 0.45 (0.44), residues: 137 loop : -0.07 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.014 0.002 TYR H 117 PHE 0.011 0.001 PHE C 322 TRP 0.014 0.001 TRP H 66 HIS 0.004 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 5867) covalent geometry : angle 0.54338 / 0.29 ( 7914) SS BOND : bond 0.00368 / 0.18 ( 3) SS BOND : angle 1.82635 / 0.96 ( 6) hydrogen bonds : bond 0.03611 / 2.53 ( 384) hydrogen bonds : angle 3.95651 / 3.00 ( 1146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2629.04 seconds wall clock time: 45 minutes 37.01 seconds (2737.01 seconds total)