Starting phenix.real_space_refine on Tue Jan 13 17:04:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0d_26256/01_2026/7u0d_26256.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0d_26256/01_2026/7u0d_26256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u0d_26256/01_2026/7u0d_26256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0d_26256/01_2026/7u0d_26256.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u0d_26256/01_2026/7u0d_26256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0d_26256/01_2026/7u0d_26256.map" } resolution = 4.8 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= -0.001 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5176 2.51 5 N 1373 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8188 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1574 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "M" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1749 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 218} Chain: "N" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 200} Chain: "O" Number of atoms: 1611 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 215, 1611 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "P" Number of atoms: 1641 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.99, per 1000 atoms: 0.24 Number of scatterers: 8188 At special positions: 0 Unit cell: (93.195, 130.815, 139.365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1603 8.00 N 1373 7.00 C 5176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS M 153 " - pdb=" SG CYS M 209 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 138 " - pdb=" SG CYS N 197 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 97 " - pdb=" SG CYS O 100B" distance=2.03 Simple disulfide: pdb=" SG CYS O 140 " - pdb=" SG CYS O 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 194 " 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=1, symmetry=0 Links applied NAG-ASN " NAG B 601 " - " ASN B 343 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 320.0 milliseconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 9.2% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.084A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.549A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 62 through 65 removed outlier: 3.524A pdb=" N LYS M 65 " --> pdb=" O ASP M 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 62 through 65' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'M' and resid 140 through 144 removed outlier: 3.841A pdb=" N THR M 144 " --> pdb=" O SER M 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 202 No H-bonds generated for 'chain 'M' and resid 200 through 202' Processing helix chain 'N' and resid 30 through 34 Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'N' and resid 125 through 131 Processing helix chain 'N' and resid 185 through 192 removed outlier: 3.762A pdb=" N HIS N 192 " --> pdb=" O GLN N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 216 Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'P' and resid 121 through 126 removed outlier: 3.508A pdb=" N GLN P 124 " --> pdb=" O SER P 121 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU P 125 " --> pdb=" O ASP P 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.992A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.575A pdb=" N GLY M 10 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL M 50 " --> pdb=" O TYR M 59 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR M 59 " --> pdb=" O VAL M 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.575A pdb=" N GLY M 10 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL M 115 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 133 through 137 removed outlier: 6.078A pdb=" N TYR M 189 " --> pdb=" O ASP M 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 133 through 137 removed outlier: 6.078A pdb=" N TYR M 189 " --> pdb=" O ASP M 157 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER M 190 " --> pdb=" O VAL M 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 164 through 167 removed outlier: 4.447A pdb=" N TYR M 207 " --> pdb=" O VAL M 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.472A pdb=" N PHE N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLN N 39 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N THR N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.472A pdb=" N PHE N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 118 through 122 removed outlier: 6.025A pdb=" N TYR N 176 " --> pdb=" O ASP N 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 118 through 122 removed outlier: 6.025A pdb=" N TYR N 176 " --> pdb=" O ASP N 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 157 through 158 Processing sheet with id=AB5, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.819A pdb=" N GLU O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'O' and resid 34 through 39 removed outlier: 5.697A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 93 through 94 Processing sheet with id=AB9, first strand: chain 'O' and resid 120 through 124 removed outlier: 3.812A pdb=" N GLY O 139 " --> pdb=" O LEU O 124 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 151 through 152 removed outlier: 4.350A pdb=" N THR O 151 " --> pdb=" O ASN O 199 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN O 199 " --> pdb=" O THR O 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.967A pdb=" N LEU P 11 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 18 through 24 Processing sheet with id=AC4, first strand: chain 'P' and resid 53 through 54 removed outlier: 4.266A pdb=" N SER P 53 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR P 49 " --> pdb=" O SER P 53 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU P 47 " --> pdb=" O TRP P 35 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 131 through 135 Processing sheet with id=AC6, first strand: chain 'P' and resid 146 through 148 273 hydrogen bonds defined for protein. 633 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: 1.14 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.44: 3713 1.44 - 1.65: 4627 1.65 - 1.87: 46 1.87 - 2.08: 2 2.08 - 2.29: 2 Bond restraints: 8390 Sorted by residual: bond pdb=" CD2 TYR O 145 " pdb=" CE2 TYR O 145 " ideal model delta sigma weight residual 1.382 2.292 -0.910 3.00e-02 1.11e+03 9.20e+02 bond pdb=" CD1 TYR O 145 " pdb=" CE1 TYR O 145 " ideal model delta sigma weight residual 1.382 2.277 -0.895 3.00e-02 1.11e+03 8.91e+02 bond pdb=" CE2 TYR O 145 " pdb=" CZ TYR O 145 " ideal model delta sigma weight residual 1.378 1.940 -0.562 2.40e-02 1.74e+03 5.49e+02 bond pdb=" CE1 TYR O 145 " pdb=" CZ TYR O 145 " ideal model delta sigma weight residual 1.378 1.923 -0.545 2.40e-02 1.74e+03 5.16e+02 bond pdb=" CG TYR O 145 " pdb=" CD1 TYR O 145 " ideal model delta sigma weight residual 1.389 1.854 -0.465 2.10e-02 2.27e+03 4.90e+02 ... (remaining 8385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.78: 11403 5.78 - 11.57: 20 11.57 - 17.35: 1 17.35 - 23.14: 0 23.14 - 28.92: 1 Bond angle restraints: 11425 Sorted by residual: angle pdb=" C TYR O 176 " pdb=" N SER O 177 " pdb=" CA SER O 177 " ideal model delta sigma weight residual 122.99 151.91 -28.92 1.41e+00 5.03e-01 4.21e+02 angle pdb=" CA PRO M 198 " pdb=" N PRO M 198 " pdb=" CD PRO M 198 " ideal model delta sigma weight residual 112.00 98.13 13.87 1.40e+00 5.10e-01 9.81e+01 angle pdb=" CA TYR O 176 " pdb=" C TYR O 176 " pdb=" O TYR O 176 " ideal model delta sigma weight residual 120.70 111.54 9.16 1.08e+00 8.57e-01 7.19e+01 angle pdb=" CA PRO B 521 " pdb=" N PRO B 521 " pdb=" CD PRO B 521 " ideal model delta sigma weight residual 112.00 104.30 7.70 1.40e+00 5.10e-01 3.03e+01 angle pdb=" C SER O 177 " pdb=" CA SER O 177 " pdb=" CB SER O 177 " ideal model delta sigma weight residual 109.71 100.98 8.73 1.83e+00 2.99e-01 2.27e+01 ... (remaining 11420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.95: 4887 31.95 - 63.90: 100 63.90 - 95.85: 8 95.85 - 127.80: 0 127.80 - 159.75: 1 Dihedral angle restraints: 4996 sinusoidal: 1907 harmonic: 3089 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 30.20 62.80 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CA VAL P 110 " pdb=" C VAL P 110 " pdb=" N ALA P 111 " pdb=" CA ALA P 111 " ideal model delta harmonic sigma weight residual 180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ARG B 403 " pdb=" C ARG B 403 " pdb=" N GLY B 404 " pdb=" CA GLY B 404 " ideal model delta harmonic sigma weight residual -180.00 -151.27 -28.73 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 4993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1090 0.069 - 0.138: 176 0.138 - 0.208: 11 0.208 - 0.277: 0 0.277 - 0.346: 1 Chirality restraints: 1278 Sorted by residual: chirality pdb=" CB ILE P 2 " pdb=" CA ILE P 2 " pdb=" CG1 ILE P 2 " pdb=" CG2 ILE P 2 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA MET M 113 " pdb=" N MET M 113 " pdb=" C MET M 113 " pdb=" CB MET M 113 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PRO M 198 " pdb=" N PRO M 198 " pdb=" C PRO M 198 " pdb=" CB PRO M 198 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1275 not shown) Planarity restraints: 1462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.105 5.00e-02 4.00e+02 1.55e-01 3.83e+01 pdb=" N PRO B 521 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 197 " -0.085 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO M 198 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO M 198 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO M 198 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA P 112 " 0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO P 113 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO P 113 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO P 113 " 0.049 5.00e-02 4.00e+02 ... (remaining 1459 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 158 2.63 - 3.20: 7759 3.20 - 3.77: 12535 3.77 - 4.33: 16763 4.33 - 4.90: 26098 Nonbonded interactions: 63313 Sorted by model distance: nonbonded pdb=" CD2 TYR O 145 " pdb=" N SER O 177 " model vdw 2.065 2.736 nonbonded pdb=" OG SER P 12 " pdb=" NH1 ARG P 107 " model vdw 2.091 3.120 nonbonded pdb=" OH TYR O 145 " pdb=" O VAL O 169 " model vdw 2.142 3.040 nonbonded pdb=" O SER O 32 " pdb=" N VAL O 52 " model vdw 2.146 3.120 nonbonded pdb=" CD1 TYR O 145 " pdb=" N SER O 177 " model vdw 2.149 2.736 ... (remaining 63308 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.760 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 0.019 0.910 8404 Z= 0.895 Angle : 0.857 28.922 11452 Z= 0.481 Chirality : 0.049 0.346 1278 Planarity : 0.008 0.155 1461 Dihedral : 13.070 159.746 2990 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.68 % Favored : 90.13 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.45 % 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: -1.37 (0.27), residues: 1054 helix: -2.20 (0.79), residues: 43 sheet: -0.22 (0.27), residues: 388 loop : -1.28 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 108 TYR 0.041 0.002 TYR O 145 PHE 0.017 0.002 PHE M 68 TRP 0.016 0.002 TRP N 189 HIS 0.004 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.01856 ( 8390) covalent geometry : angle 0.85460 (11425) SS BOND : bond 0.00279 ( 12) SS BOND : angle 1.59959 ( 24) hydrogen bonds : bond 0.16169 ( 235) hydrogen bonds : angle 6.69768 ( 633) Misc. bond : bond 0.45039 ( 1) link_NAG-ASN : bond 0.00215 ( 1) link_NAG-ASN : angle 1.63851 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 34 MET cc_start: 0.7860 (mmm) cc_final: 0.7655 (mmt) REVERT: M 157 ASP cc_start: 0.9343 (t70) cc_final: 0.9066 (p0) REVERT: N 142 ASP cc_start: 0.8975 (m-30) cc_final: 0.8681 (m-30) REVERT: P 60 ASP cc_start: 0.8730 (p0) cc_final: 0.8427 (p0) REVERT: P 149 LYS cc_start: 0.9646 (tptt) cc_final: 0.9284 (tptp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1048 time to fit residues: 9.7080 Evaluate side-chains 42 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0040 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 171 GLN N 174 ASN N 188 GLN O 171 GLN P 158 ASN P 160 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.035031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.023410 restraints weight = 134006.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.024424 restraints weight = 91736.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.024617 restraints weight = 60258.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.024721 restraints weight = 49008.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.024929 restraints weight = 45553.408| |-----------------------------------------------------------------------------| r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 8404 Z= 0.342 Angle : 0.926 16.555 11452 Z= 0.491 Chirality : 0.050 0.214 1278 Planarity : 0.008 0.084 1461 Dihedral : 6.588 33.559 1179 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 35.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.63 % Favored : 89.09 % Rotamer: Outliers : 0.33 % Allowed : 9.98 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.83 (0.26), residues: 1054 helix: -2.30 (0.79), residues: 42 sheet: -0.32 (0.27), residues: 352 loop : -1.72 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 355 TYR 0.063 0.004 TYR O 145 PHE 0.039 0.003 PHE O 146 TRP 0.029 0.003 TRP O 154 HIS 0.008 0.002 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00706 ( 8390) covalent geometry : angle 0.92326 (11425) SS BOND : bond 0.00671 ( 12) SS BOND : angle 1.67983 ( 24) hydrogen bonds : bond 0.04381 ( 235) hydrogen bonds : angle 6.94418 ( 633) Misc. bond : bond 0.02016 ( 1) link_NAG-ASN : bond 0.00144 ( 1) link_NAG-ASN : angle 1.46857 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.323 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 39 average time/residue: 0.1022 time to fit residues: 5.7141 Evaluate side-chains 24 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 16 optimal weight: 0.0270 chunk 29 optimal weight: 0.1980 chunk 71 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 104 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN N 188 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.038319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.026154 restraints weight = 122134.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.026917 restraints weight = 79396.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.027406 restraints weight = 55522.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.027602 restraints weight = 43339.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.027978 restraints weight = 39735.103| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8404 Z= 0.131 Angle : 0.727 10.685 11452 Z= 0.369 Chirality : 0.047 0.193 1278 Planarity : 0.005 0.068 1461 Dihedral : 5.805 38.112 1179 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.54 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.63 (0.26), residues: 1054 helix: -2.15 (0.78), residues: 42 sheet: -0.33 (0.26), residues: 375 loop : -1.52 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 107 TYR 0.037 0.002 TYR O 145 PHE 0.016 0.001 PHE P 62 TRP 0.014 0.001 TRP P 148 HIS 0.010 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8390) covalent geometry : angle 0.72458 (11425) SS BOND : bond 0.00440 ( 12) SS BOND : angle 1.31332 ( 24) hydrogen bonds : bond 0.03499 ( 235) hydrogen bonds : angle 5.92418 ( 633) Misc. bond : bond 0.02247 ( 1) link_NAG-ASN : bond 0.00315 ( 1) link_NAG-ASN : angle 2.62296 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1306 time to fit residues: 8.2704 Evaluate side-chains 27 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 14 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 0.0980 chunk 53 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.037357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.025223 restraints weight = 123897.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.026019 restraints weight = 82427.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.026391 restraints weight = 57216.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.026526 restraints weight = 44360.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.026787 restraints weight = 41872.858| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8404 Z= 0.142 Angle : 0.695 11.841 11452 Z= 0.354 Chirality : 0.046 0.277 1278 Planarity : 0.006 0.088 1461 Dihedral : 5.570 38.944 1179 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.49 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.56 (0.26), residues: 1054 helix: -2.06 (0.81), residues: 42 sheet: -0.29 (0.27), residues: 369 loop : -1.45 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 142 TYR 0.041 0.002 TYR O 145 PHE 0.012 0.001 PHE P 62 TRP 0.013 0.002 TRP O 154 HIS 0.009 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8390) covalent geometry : angle 0.69170 (11425) SS BOND : bond 0.00438 ( 12) SS BOND : angle 1.49509 ( 24) hydrogen bonds : bond 0.03056 ( 235) hydrogen bonds : angle 5.90363 ( 633) Misc. bond : bond 0.02406 ( 1) link_NAG-ASN : bond 0.00190 ( 1) link_NAG-ASN : angle 2.12382 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 113 MET cc_start: 0.9324 (pmm) cc_final: 0.9116 (pmm) REVERT: N 94 MET cc_start: 0.9786 (mmp) cc_final: 0.9507 (mmm) REVERT: O 90 TYR cc_start: 0.9645 (m-10) cc_final: 0.9365 (m-10) REVERT: P 36 TYR cc_start: 0.9505 (m-10) cc_final: 0.9281 (m-80) REVERT: P 91 TYR cc_start: 0.8993 (m-80) cc_final: 0.8735 (m-80) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1001 time to fit residues: 5.9290 Evaluate side-chains 28 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.037409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.025276 restraints weight = 122691.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.026059 restraints weight = 84738.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.026545 restraints weight = 56550.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.026660 restraints weight = 44237.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.026925 restraints weight = 41824.689| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8404 Z= 0.132 Angle : 0.675 11.403 11452 Z= 0.344 Chirality : 0.046 0.208 1278 Planarity : 0.005 0.064 1461 Dihedral : 5.494 42.573 1179 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.68 % Favored : 90.04 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.52 (0.26), residues: 1054 helix: -2.04 (0.82), residues: 42 sheet: -0.27 (0.27), residues: 367 loop : -1.43 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 142 TYR 0.048 0.002 TYR O 145 PHE 0.014 0.001 PHE P 62 TRP 0.011 0.001 TRP P 148 HIS 0.007 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8390) covalent geometry : angle 0.67271 (11425) SS BOND : bond 0.00585 ( 12) SS BOND : angle 1.23328 ( 24) hydrogen bonds : bond 0.02885 ( 235) hydrogen bonds : angle 5.67350 ( 633) Misc. bond : bond 0.02407 ( 1) link_NAG-ASN : bond 0.00238 ( 1) link_NAG-ASN : angle 2.15491 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 92 LEU cc_start: 0.9825 (tt) cc_final: 0.9316 (tt) REVERT: N 94 MET cc_start: 0.9789 (mmp) cc_final: 0.9197 (mpp) REVERT: P 36 TYR cc_start: 0.9487 (m-10) cc_final: 0.9261 (m-80) REVERT: P 91 TYR cc_start: 0.8897 (m-80) cc_final: 0.8609 (m-80) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1004 time to fit residues: 5.5891 Evaluate side-chains 24 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.037266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.025543 restraints weight = 125082.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.026292 restraints weight = 84249.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.026678 restraints weight = 58995.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.026843 restraints weight = 46248.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.027158 restraints weight = 43188.187| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8404 Z= 0.134 Angle : 0.679 11.056 11452 Z= 0.344 Chirality : 0.046 0.190 1278 Planarity : 0.006 0.077 1461 Dihedral : 5.427 44.601 1179 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.20 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.51 (0.26), residues: 1054 helix: -2.01 (0.83), residues: 42 sheet: -0.29 (0.27), residues: 375 loop : -1.41 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 142 TYR 0.054 0.001 TYR O 145 PHE 0.016 0.001 PHE P 62 TRP 0.012 0.002 TRP O 154 HIS 0.006 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8390) covalent geometry : angle 0.67660 (11425) SS BOND : bond 0.00390 ( 12) SS BOND : angle 1.26013 ( 24) hydrogen bonds : bond 0.02877 ( 235) hydrogen bonds : angle 5.61382 ( 633) Misc. bond : bond 0.02480 ( 1) link_NAG-ASN : bond 0.00225 ( 1) link_NAG-ASN : angle 2.08103 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 113 MET cc_start: 0.9305 (pmm) cc_final: 0.9104 (pmm) REVERT: N 92 LEU cc_start: 0.9809 (tt) cc_final: 0.9575 (tt) REVERT: N 94 MET cc_start: 0.9778 (mmp) cc_final: 0.9515 (mmm) REVERT: P 91 TYR cc_start: 0.8894 (m-80) cc_final: 0.8431 (m-80) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1137 time to fit residues: 5.7964 Evaluate side-chains 25 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.037488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.025610 restraints weight = 124599.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.026319 restraints weight = 83896.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.026786 restraints weight = 58393.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.026940 restraints weight = 45494.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.027200 restraints weight = 42663.476| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8404 Z= 0.125 Angle : 0.662 10.661 11452 Z= 0.337 Chirality : 0.046 0.287 1278 Planarity : 0.005 0.059 1461 Dihedral : 5.341 45.679 1179 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.20 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.47 (0.27), residues: 1054 helix: -2.01 (0.83), residues: 42 sheet: -0.34 (0.27), residues: 386 loop : -1.33 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 403 TYR 0.057 0.001 TYR O 145 PHE 0.015 0.001 PHE P 62 TRP 0.011 0.001 TRP P 148 HIS 0.005 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8390) covalent geometry : angle 0.65998 (11425) SS BOND : bond 0.00411 ( 12) SS BOND : angle 1.16413 ( 24) hydrogen bonds : bond 0.02835 ( 235) hydrogen bonds : angle 5.53978 ( 633) Misc. bond : bond 0.02494 ( 1) link_NAG-ASN : bond 0.00264 ( 1) link_NAG-ASN : angle 2.13012 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 109 TYR cc_start: 0.8256 (p90) cc_final: 0.8025 (p90) REVERT: P 91 TYR cc_start: 0.8009 (m-80) cc_final: 0.7780 (m-80) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1134 time to fit residues: 6.1826 Evaluate side-chains 26 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 102 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 39 optimal weight: 8.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.037651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.025992 restraints weight = 125536.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.026686 restraints weight = 83359.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.027026 restraints weight = 59793.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.027229 restraints weight = 46989.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.027293 restraints weight = 43530.824| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8404 Z= 0.121 Angle : 0.671 10.475 11452 Z= 0.338 Chirality : 0.046 0.313 1278 Planarity : 0.005 0.057 1461 Dihedral : 5.278 46.049 1179 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.73 % Favored : 90.99 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.44 (0.27), residues: 1054 helix: -2.01 (0.83), residues: 42 sheet: -0.23 (0.27), residues: 379 loop : -1.36 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 107 TYR 0.058 0.001 TYR O 145 PHE 0.016 0.001 PHE P 62 TRP 0.010 0.001 TRP P 148 HIS 0.005 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8390) covalent geometry : angle 0.66926 (11425) SS BOND : bond 0.00399 ( 12) SS BOND : angle 1.08997 ( 24) hydrogen bonds : bond 0.02788 ( 235) hydrogen bonds : angle 5.41373 ( 633) Misc. bond : bond 0.02498 ( 1) link_NAG-ASN : bond 0.00257 ( 1) link_NAG-ASN : angle 2.17387 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 34 MET cc_start: 0.9633 (mmm) cc_final: 0.9429 (mmm) REVERT: N 94 MET cc_start: 0.9760 (mmp) cc_final: 0.9495 (mmm) REVERT: O 80 MET cc_start: 0.9093 (tmm) cc_final: 0.8564 (tmm) REVERT: P 91 TYR cc_start: 0.8773 (m-80) cc_final: 0.8384 (m-80) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1100 time to fit residues: 5.8706 Evaluate side-chains 26 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.037892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.026340 restraints weight = 124602.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.026789 restraints weight = 82736.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.027312 restraints weight = 60380.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.027402 restraints weight = 46219.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.027469 restraints weight = 43505.360| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8404 Z= 0.120 Angle : 0.670 10.376 11452 Z= 0.336 Chirality : 0.047 0.325 1278 Planarity : 0.005 0.059 1461 Dihedral : 5.225 46.376 1179 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.58 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.38 (0.27), residues: 1054 helix: -1.97 (0.84), residues: 42 sheet: -0.18 (0.27), residues: 388 loop : -1.35 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 107 TYR 0.059 0.001 TYR O 145 PHE 0.016 0.001 PHE P 62 TRP 0.010 0.001 TRP P 148 HIS 0.003 0.001 HIS P 198 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8390) covalent geometry : angle 0.66809 (11425) SS BOND : bond 0.00382 ( 12) SS BOND : angle 1.05857 ( 24) hydrogen bonds : bond 0.02768 ( 235) hydrogen bonds : angle 5.34453 ( 633) Misc. bond : bond 0.02510 ( 1) link_NAG-ASN : bond 0.00277 ( 1) link_NAG-ASN : angle 2.18466 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 94 MET cc_start: 0.9765 (mmp) cc_final: 0.9524 (mmm) REVERT: O 73 MET cc_start: 0.9596 (ppp) cc_final: 0.9174 (mmt) REVERT: O 80 MET cc_start: 0.9098 (tmm) cc_final: 0.8584 (tmm) REVERT: P 91 TYR cc_start: 0.8731 (m-80) cc_final: 0.8355 (m-80) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1130 time to fit residues: 6.5586 Evaluate side-chains 27 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 chunk 38 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 GLN ** P 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.035873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.024284 restraints weight = 133606.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.024714 restraints weight = 91336.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.025293 restraints weight = 63755.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.025409 restraints weight = 49020.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.025542 restraints weight = 46686.294| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8404 Z= 0.200 Angle : 0.730 10.055 11452 Z= 0.376 Chirality : 0.047 0.367 1278 Planarity : 0.005 0.056 1461 Dihedral : 5.726 46.817 1179 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 26.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.29 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.55 (0.26), residues: 1054 helix: -2.04 (0.84), residues: 42 sheet: -0.35 (0.27), residues: 366 loop : -1.40 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 466 TYR 0.058 0.002 TYR O 145 PHE 0.021 0.002 PHE B 392 TRP 0.021 0.002 TRP O 154 HIS 0.005 0.002 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8390) covalent geometry : angle 0.72744 (11425) SS BOND : bond 0.00510 ( 12) SS BOND : angle 1.35184 ( 24) hydrogen bonds : bond 0.03025 ( 235) hydrogen bonds : angle 5.80129 ( 633) Misc. bond : bond 0.02376 ( 1) link_NAG-ASN : bond 0.00151 ( 1) link_NAG-ASN : angle 1.82319 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: O 73 MET cc_start: 0.9035 (ppp) cc_final: 0.8640 (mmt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1025 time to fit residues: 4.5938 Evaluate side-chains 20 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 0.0570 chunk 96 optimal weight: 0.0970 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 71 ASN N 188 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.037359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.024827 restraints weight = 125649.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.025655 restraints weight = 89815.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.026194 restraints weight = 59794.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.026357 restraints weight = 48327.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.026648 restraints weight = 44499.855| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8404 Z= 0.122 Angle : 0.687 10.192 11452 Z= 0.347 Chirality : 0.047 0.336 1278 Planarity : 0.005 0.061 1461 Dihedral : 5.442 46.742 1179 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.63 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.41 (0.27), residues: 1054 helix: -2.01 (0.84), residues: 42 sheet: -0.26 (0.27), residues: 384 loop : -1.32 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 107 TYR 0.060 0.001 TYR O 145 PHE 0.018 0.001 PHE P 62 TRP 0.015 0.001 TRP P 148 HIS 0.003 0.001 HIS P 198 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8390) covalent geometry : angle 0.68492 (11425) SS BOND : bond 0.00403 ( 12) SS BOND : angle 1.17220 ( 24) hydrogen bonds : bond 0.02790 ( 235) hydrogen bonds : angle 5.43857 ( 633) Misc. bond : bond 0.02514 ( 1) link_NAG-ASN : bond 0.00359 ( 1) link_NAG-ASN : angle 2.24791 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2116.08 seconds wall clock time: 37 minutes 26.28 seconds (2246.28 seconds total)