Starting phenix.real_space_refine on Fri Dec 27 18:37:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e1m_27825/12_2024/8e1m_27825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e1m_27825/12_2024/8e1m_27825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e1m_27825/12_2024/8e1m_27825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e1m_27825/12_2024/8e1m_27825.map" model { file = "/net/cci-nas-00/data/ceres_data/8e1m_27825/12_2024/8e1m_27825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e1m_27825/12_2024/8e1m_27825.cif" } resolution = 2.9 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= 0.003 sd= 0.027 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 3627 2.51 5 N 980 2.21 5 O 1052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 5691 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 955 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 958 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1921 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 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: 4.29, per 1000 atoms: 0.75 Number of scatterers: 5691 At special positions: 0 Unit cell: (93.45, 122.85, 79.8, 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 1052 8.00 N 980 7.00 C 3627 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=2.04 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: 1.48 Conformation dependent library (CDL) restraints added in 898.6 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: 22 helices and 9 sheets defined 53.3% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 9 through 41 removed outlier: 3.970A pdb=" N ILE A 14 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 4.199A pdb=" N ARG A 46 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 84 Proline residue: A 59 - end of helix removed outlier: 3.681A pdb=" N SER A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.694A pdb=" N ILE A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 138 removed outlier: 3.608A pdb=" N ARG A 112 " --> pdb=" O TRP A 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 123 removed outlier: 3.717A pdb=" N ASP B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 169 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: 3.525A pdb=" N GLY B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 3.654A 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 Processing helix chain 'C' and resid 166 through 172 removed outlier: 3.767A pdb=" N SER C 169 " --> pdb=" O GLY C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 removed outlier: 3.525A pdb=" N LYS C 183 " --> pdb=" O GLN C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.662A 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 308 Processing helix chain 'C' and resid 309 through 317 removed outlier: 3.870A pdb=" N LYS C 315 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 335 removed outlier: 3.502A pdb=" N VAL C 324 " --> pdb=" O ALA C 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.830A pdb=" N THR H 109 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.045A pdb=" N ILE C 362 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS C 355 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL C 364 " --> pdb=" O SER C 353 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 366 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE C 351 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY C 368 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL C 349 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C 345 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 374 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 5.753A 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: 5.005A pdb=" N ARG C 404 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN C 375 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN C 392 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N TYR C 377 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLU C 390 " --> pdb=" O TYR C 377 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N LYS C 379 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 12.788A pdb=" N GLY C 388 " --> pdb=" O LYS C 379 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 421 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR C 403 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE C 419 " --> pdb=" O THR C 403 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.531A pdb=" N ASP L 94 " --> pdb=" O SER L 91 " (cutoff:3.500A) removed outlier: 3.534A 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: 7.084A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N MET L 57 " --> pdb=" O TYR L 73 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR L 73 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 30 through 33 removed outlier: 7.084A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 50 through 51 Processing sheet with id=AA7, first strand: chain 'H' and resid 22 through 26 Processing sheet with id=AA8, first strand: chain 'H' and resid 76 through 78 removed outlier: 6.843A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL H 69 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY H 52 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR H 125 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 76 through 78 removed outlier: 6.843A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL H 69 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY H 52 " --> pdb=" O TYR H 117 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1128 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: 1.50 Time building geometry restraints manager: 1.70 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: 1826 1.34 - 1.46: 1421 1.46 - 1.59: 2506 1.59 - 1.71: 6 1.71 - 1.84: 46 Bond restraints: 5805 Sorted by residual: bond pdb=" CA7 CDL A 301 " pdb=" OA8 CDL A 301 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.15e+02 bond pdb=" CB7 CDL A 301 " pdb=" OB8 CDL A 301 " ideal model delta sigma weight residual 1.334 1.446 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" CB5 CDL A 301 " pdb=" OB6 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=" CA5 CDL A 301 " pdb=" OA6 CDL A 301 " ideal model delta sigma weight residual 1.342 1.449 -0.107 1.50e-02 4.44e+03 5.12e+01 bond pdb=" C8 PTY B 301 " pdb=" O7 PTY B 301 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.77e+01 ... (remaining 5800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 7661 2.19 - 4.38: 139 4.38 - 6.57: 31 6.57 - 8.76: 3 8.76 - 10.94: 6 Bond angle restraints: 7840 Sorted by residual: angle pdb=" C51 CDL A 301 " pdb=" CB5 CDL A 301 " pdb=" OB6 CDL A 301 " ideal model delta sigma weight residual 111.33 121.20 -9.87 1.32e+00 5.72e-01 5.58e+01 angle pdb=" C11 CDL A 301 " pdb=" CA5 CDL A 301 " pdb=" OA6 CDL A 301 " ideal model delta sigma weight residual 111.33 120.23 -8.90 1.32e+00 5.72e-01 4.53e+01 angle pdb=" C31 CDL A 301 " pdb=" CA7 CDL A 301 " pdb=" OA8 CDL A 301 " ideal model delta sigma weight residual 111.64 121.14 -9.50 1.65e+00 3.69e-01 3.33e+01 angle pdb=" OB6 CDL A 301 " pdb=" CB5 CDL A 301 " pdb=" OB7 CDL A 301 " ideal model delta sigma weight residual 123.92 118.41 5.51 1.00e+00 9.92e-01 3.01e+01 angle pdb=" C71 CDL A 301 " pdb=" CB7 CDL A 301 " pdb=" OB8 CDL A 301 " ideal model delta sigma weight residual 111.64 120.27 -8.63 1.65e+00 3.69e-01 2.75e+01 ... (remaining 7835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.84: 3219 23.84 - 47.68: 188 47.68 - 71.52: 24 71.52 - 95.36: 5 95.36 - 119.20: 1 Dihedral angle restraints: 3437 sinusoidal: 1309 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 -124.76 38.76 1 1.00e+01 1.00e-02 2.11e+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 -53.87 119.20 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" CA ILE B 166 " pdb=" C ILE B 166 " pdb=" N ASP B 167 " pdb=" CA ASP B 167 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 3434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 508 0.031 - 0.063: 235 0.063 - 0.094: 68 0.094 - 0.125: 38 0.125 - 0.156: 7 Chirality restraints: 856 Sorted by residual: 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 2.59 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA ILE C 362 " pdb=" N ILE C 362 " pdb=" C ILE C 362 " pdb=" CB ILE C 362 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-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 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 853 not shown) Planarity restraints: 1003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 145 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO B 146 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 8 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 9 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 67 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO L 68 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO L 68 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 68 " 0.021 5.00e-02 4.00e+02 ... (remaining 1000 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 263 2.72 - 3.27: 5714 3.27 - 3.81: 9339 3.81 - 4.36: 12101 4.36 - 4.90: 20858 Nonbonded interactions: 48275 Sorted by model distance: nonbonded pdb=" O LEU B 97 " pdb=" OG1 THR B 101 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASP L 50 " pdb=" OG SER L 55 " model vdw 2.181 3.040 nonbonded pdb=" OG SER L 48 " pdb=" OD2 ASP L 50 " model vdw 2.185 3.040 nonbonded pdb=" NZ LYS L 63 " pdb=" O ASP L 105 " model vdw 2.231 3.120 nonbonded pdb=" NZ LYS C 278 " pdb=" O PRO C 282 " model vdw 2.249 3.120 ... (remaining 48270 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: 0.970 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 5805 Z= 0.456 Angle : 0.765 10.945 7840 Z= 0.411 Chirality : 0.043 0.156 856 Planarity : 0.004 0.049 1003 Dihedral : 14.841 119.204 2076 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.83 (0.31), residues: 748 helix: -0.30 (0.26), residues: 370 sheet: -0.54 (0.45), residues: 142 loop : -0.63 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 66 HIS 0.003 0.001 HIS B 173 PHE 0.012 0.002 PHE A 96 TYR 0.016 0.002 TYR H 117 ARG 0.004 0.001 ARG L 38 *********************** 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 111 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.7366 (m-80) cc_final: 0.6891 (m-80) outliers start: 0 outliers final: 2 residues processed: 111 average time/residue: 1.1962 time to fit residues: 138.9613 Evaluate side-chains 85 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain B residue 161 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN L 66 GLN H 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5805 Z= 0.272 Angle : 0.604 8.133 7840 Z= 0.314 Chirality : 0.043 0.150 856 Planarity : 0.005 0.044 1003 Dihedral : 10.280 64.738 920 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.48 % Allowed : 10.89 % Favored : 87.64 % 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: 0.79 (0.32), residues: 748 helix: 1.42 (0.26), residues: 372 sheet: -0.21 (0.45), residues: 142 loop : -0.30 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 108 HIS 0.004 0.001 HIS A 33 PHE 0.017 0.001 PHE C 322 TYR 0.013 0.001 TYR H 117 ARG 0.009 0.001 ARG C 170 *********************** 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 102 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: B 162 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8284 (mp) REVERT: L 127 LYS cc_start: 0.8388 (tttp) cc_final: 0.8067 (tttp) REVERT: L 129 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6619 (mt-10) outliers start: 8 outliers final: 3 residues processed: 95 average time/residue: 1.1164 time to fit residues: 111.6324 Evaluate side-chains 88 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN L 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5805 Z= 0.261 Angle : 0.554 8.637 7840 Z= 0.288 Chirality : 0.043 0.142 856 Planarity : 0.004 0.042 1003 Dihedral : 9.777 66.368 916 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.03 % Allowed : 12.73 % Favored : 85.24 % 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: 1.41 (0.32), residues: 748 helix: 2.13 (0.26), residues: 372 sheet: -0.13 (0.45), residues: 142 loop : -0.26 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 32 HIS 0.004 0.001 HIS A 33 PHE 0.014 0.001 PHE A 96 TYR 0.012 0.001 TYR H 117 ARG 0.005 0.000 ARG C 170 *********************** 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 103 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: B 162 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8335 (mp) REVERT: L 127 LYS cc_start: 0.8289 (tttp) cc_final: 0.7979 (tttp) REVERT: L 129 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6536 (mt-10) outliers start: 11 outliers final: 5 residues processed: 96 average time/residue: 1.0694 time to fit residues: 108.1969 Evaluate side-chains 90 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.0370 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 64 optimal weight: 0.0970 chunk 19 optimal weight: 0.8980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS C 335 GLN L 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5805 Z= 0.163 Angle : 0.526 9.832 7840 Z= 0.268 Chirality : 0.042 0.157 856 Planarity : 0.004 0.043 1003 Dihedral : 9.167 64.707 916 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.40 % Allowed : 15.50 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.32), residues: 748 helix: 2.38 (0.26), residues: 373 sheet: 0.04 (0.45), residues: 142 loop : -0.11 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 32 HIS 0.003 0.001 HIS A 33 PHE 0.012 0.001 PHE A 96 TYR 0.009 0.001 TYR H 117 ARG 0.003 0.000 ARG C 181 *********************** 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 110 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: B 162 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8316 (mp) REVERT: B 198 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7568 (mmt) REVERT: L 127 LYS cc_start: 0.8236 (tttp) cc_final: 0.7947 (tttp) REVERT: L 129 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6446 (mt-10) outliers start: 13 outliers final: 6 residues processed: 104 average time/residue: 1.0704 time to fit residues: 117.3647 Evaluate side-chains 97 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 0.0010 chunk 18 optimal weight: 1.9990 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5805 Z= 0.300 Angle : 0.578 9.155 7840 Z= 0.295 Chirality : 0.044 0.166 856 Planarity : 0.004 0.041 1003 Dihedral : 9.385 64.705 916 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.21 % Allowed : 16.24 % Favored : 81.55 % 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: 1.87 (0.32), residues: 748 helix: 2.47 (0.27), residues: 373 sheet: 0.19 (0.47), residues: 135 loop : -0.05 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.003 0.001 HIS B 140 PHE 0.012 0.001 PHE A 96 TYR 0.018 0.002 TYR B 159 ARG 0.003 0.000 ARG C 181 *********************** 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 105 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: B 162 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8353 (mp) outliers start: 12 outliers final: 5 residues processed: 98 average time/residue: 1.0982 time to fit residues: 113.3256 Evaluate side-chains 94 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN L 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5805 Z= 0.174 Angle : 0.536 10.692 7840 Z= 0.272 Chirality : 0.042 0.174 856 Planarity : 0.004 0.041 1003 Dihedral : 8.949 65.275 916 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.21 % Allowed : 16.05 % Favored : 81.73 % 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: 2.03 (0.32), residues: 748 helix: 2.61 (0.27), residues: 373 sheet: 0.18 (0.46), residues: 142 loop : 0.07 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 32 HIS 0.002 0.001 HIS A 33 PHE 0.012 0.001 PHE A 96 TYR 0.018 0.001 TYR B 159 ARG 0.003 0.000 ARG C 181 *********************** 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 108 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: B 162 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8297 (mp) REVERT: L 129 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6734 (mt-10) outliers start: 12 outliers final: 7 residues processed: 102 average time/residue: 1.1306 time to fit residues: 121.2795 Evaluate side-chains 99 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 30.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 GLN L 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5805 Z= 0.230 Angle : 0.568 10.070 7840 Z= 0.284 Chirality : 0.043 0.192 856 Planarity : 0.003 0.041 1003 Dihedral : 8.953 64.704 916 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.21 % Allowed : 16.97 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.32), residues: 748 helix: 2.65 (0.27), residues: 373 sheet: 0.29 (0.47), residues: 135 loop : 0.07 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.003 0.001 HIS A 33 PHE 0.011 0.001 PHE A 96 TYR 0.013 0.001 TYR B 159 ARG 0.003 0.000 ARG L 85 *********************** 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 104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 131 MET cc_start: 0.7820 (mmt) cc_final: 0.7513 (mmm) REVERT: B 162 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8324 (mp) outliers start: 12 outliers final: 7 residues processed: 97 average time/residue: 1.0252 time to fit residues: 105.0077 Evaluate side-chains 97 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5805 Z= 0.252 Angle : 0.589 10.347 7840 Z= 0.293 Chirality : 0.043 0.234 856 Planarity : 0.004 0.041 1003 Dihedral : 9.016 65.114 916 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.85 % Allowed : 17.71 % Favored : 80.44 % 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: 2.13 (0.32), residues: 748 helix: 2.69 (0.27), residues: 372 sheet: 0.35 (0.47), residues: 135 loop : 0.05 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.003 0.001 HIS A 33 PHE 0.012 0.001 PHE A 96 TYR 0.013 0.001 TYR H 117 ARG 0.002 0.000 ARG L 85 *********************** 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 98 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 131 MET cc_start: 0.7794 (mmt) cc_final: 0.7504 (mmm) REVERT: B 162 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8344 (mp) REVERT: B 198 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7540 (mmm) outliers start: 10 outliers final: 6 residues processed: 94 average time/residue: 1.1098 time to fit residues: 109.8063 Evaluate side-chains 93 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5805 Z= 0.304 Angle : 0.608 10.414 7840 Z= 0.306 Chirality : 0.044 0.210 856 Planarity : 0.004 0.041 1003 Dihedral : 9.175 65.570 916 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.85 % Allowed : 17.34 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.32), residues: 748 helix: 2.59 (0.27), residues: 372 sheet: 0.41 (0.47), residues: 135 loop : 0.02 (0.42), residues: 241 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 0.012 0.001 PHE A 96 TYR 0.014 0.001 TYR H 117 ARG 0.002 0.000 ARG L 85 *********************** 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 99 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 131 MET cc_start: 0.7802 (mmt) cc_final: 0.7515 (mmm) REVERT: B 198 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7527 (mmm) outliers start: 10 outliers final: 5 residues processed: 95 average time/residue: 1.0324 time to fit residues: 103.6558 Evaluate side-chains 92 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5805 Z= 0.217 Angle : 0.588 11.213 7840 Z= 0.295 Chirality : 0.044 0.278 856 Planarity : 0.004 0.042 1003 Dihedral : 8.938 66.220 916 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.92 % Allowed : 17.71 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.32), residues: 748 helix: 2.61 (0.26), residues: 374 sheet: 0.27 (0.45), residues: 142 loop : 0.06 (0.43), residues: 232 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 96 TYR 0.011 0.001 TYR H 117 ARG 0.002 0.000 ARG C 181 ********************** 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 96 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 125 ILE cc_start: 0.9028 (mp) cc_final: 0.8798 (mp) REVERT: A 131 MET cc_start: 0.7742 (mmt) cc_final: 0.7459 (mmm) outliers start: 5 outliers final: 5 residues processed: 95 average time/residue: 1.0560 time to fit residues: 105.7379 Evaluate side-chains 91 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 0.0060 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 GLN L 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.083551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.062154 restraints weight = 12544.881| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.66 r_work: 0.2795 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5805 Z= 0.191 Angle : 0.595 11.157 7840 Z= 0.300 Chirality : 0.042 0.171 856 Planarity : 0.004 0.042 1003 Dihedral : 8.727 65.833 916 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.48 % Allowed : 18.08 % Favored : 80.44 % 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 (0.32), residues: 748 helix: 2.69 (0.27), residues: 374 sheet: 0.38 (0.46), residues: 135 loop : -0.03 (0.41), residues: 239 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 96 TYR 0.009 0.001 TYR B 159 ARG 0.002 0.000 ARG C 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2386.54 seconds wall clock time: 44 minutes 8.10 seconds (2648.10 seconds total)