Starting phenix.real_space_refine on Wed Feb 4 23:17:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cmw_45754/02_2026/9cmw_45754.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cmw_45754/02_2026/9cmw_45754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cmw_45754/02_2026/9cmw_45754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cmw_45754/02_2026/9cmw_45754.map" model { file = "/net/cci-nas-00/data/ceres_data/9cmw_45754/02_2026/9cmw_45754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cmw_45754/02_2026/9cmw_45754.cif" } resolution = 4.0 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= 0.004 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5536 atoms to isotropic. 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 19 5.16 5 C 5718 2.51 5 N 1581 2.21 5 O 1751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9069 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5996 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 27, 'TRANS': 743} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 389 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 44} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1901 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.77, per 1000 atoms: 0.20 Number of scatterers: 9069 At special positions: 0 Unit cell: (107.969, 110.107, 120.797, 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 19 16.00 O 1751 8.00 N 1581 7.00 C 5718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 438.1 milliseconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 31.0% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.828A pdb=" N VAL A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 58 removed outlier: 3.571A pdb=" N GLY A 58 " --> pdb=" O ASP A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 59 through 67 Processing helix chain 'A' and resid 105 through 115 Processing helix chain 'A' and resid 125 through 143 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.689A pdb=" N ARG A 209 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 210' Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 248 through 251 removed outlier: 4.029A pdb=" N THR A 251 " --> pdb=" O GLU A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.539A pdb=" N LEU A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 312 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 378 through 391 removed outlier: 4.152A pdb=" N ARG A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.831A pdb=" N ASP A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 650 Processing helix chain 'A' and resid 674 through 676 No H-bonds generated for 'chain 'A' and resid 674 through 676' Processing helix chain 'D' and resid 34 through 48 Processing helix chain 'D' and resid 51 through 57 removed outlier: 3.828A pdb=" N LYS D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 4.084A pdb=" N GLU D 62 " --> pdb=" O TYR D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 85 removed outlier: 3.877A pdb=" N ARG D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA D 79 " --> pdb=" O GLN D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 102 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.756A pdb=" N ALA D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.710A pdb=" N LYS D 129 " --> pdb=" O PHE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 157 removed outlier: 3.941A pdb=" N ASN D 143 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 190 removed outlier: 3.594A pdb=" N TYR D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS D 190 " --> pdb=" O ARG D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.969A pdb=" N ASN D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 230 through 245 Processing helix chain 'E' and resid 40 through 46 removed outlier: 3.706A pdb=" N VAL E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA E 45 " --> pdb=" O PRO E 41 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 46' Processing helix chain 'E' and resid 52 through 61 Processing helix chain 'E' and resid 107 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 removed outlier: 4.377A pdb=" N ASP A 73 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 98 removed outlier: 5.768A pdb=" N VAL A 162 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 95 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 164 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP A 163 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 155 " --> pdb=" O ASP A 163 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 165 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 153 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.822A pdb=" N GLN A 149 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 169 " --> pdb=" O GLN A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 180 removed outlier: 7.492A pdb=" N ILE A 255 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE A 179 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE A 257 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 258 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 241 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 274 removed outlier: 4.040A pdb=" N VAL A 338 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 325 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 400 removed outlier: 7.046A pdb=" N THR A 419 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 398 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA8, first strand: chain 'A' and resid 425 through 432 removed outlier: 3.920A pdb=" N THR A 466 " --> pdb=" O SER A 463 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 485 through 490 current: chain 'A' and resid 507 through 513 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 507 through 513 current: chain 'A' and resid 526 through 539 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 526 through 539 current: chain 'A' and resid 562 through 579 Processing sheet with id=AA9, first strand: chain 'A' and resid 617 through 619 removed outlier: 4.224A pdb=" N MET A 628 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 692 " --> pdb=" O MET A 628 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 693 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 710 " --> pdb=" O LEU A 693 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 632 through 635 Processing sheet with id=AB2, first strand: chain 'A' and resid 670 through 672 removed outlier: 3.518A pdb=" N VAL A 671 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.743A pdb=" N GLU E 105 " --> pdb=" O THR E 93 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG E 103 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU E 97 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 79 through 82 removed outlier: 6.812A pdb=" N THR E 80 " --> pdb=" O LYS E 87 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 85 " --> pdb=" O ARG E 82 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 918 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: 1.34 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1657 1.33 - 1.45: 2400 1.45 - 1.57: 5158 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 9253 Sorted by residual: bond pdb=" N THR E 71 " pdb=" CA THR E 71 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.57e+00 bond pdb=" CA ALA C 60 " pdb=" CB ALA C 60 " ideal model delta sigma weight residual 1.530 1.487 0.043 1.69e-02 3.50e+03 6.50e+00 bond pdb=" C PRO C 59 " pdb=" O PRO C 59 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.28e-02 6.10e+03 6.25e+00 bond pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 1.470 1.440 0.031 1.37e-02 5.33e+03 5.02e+00 bond pdb=" CA SER C 62 " pdb=" CB SER C 62 " ideal model delta sigma weight residual 1.530 1.494 0.036 1.69e-02 3.50e+03 4.60e+00 ... (remaining 9248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 12329 2.29 - 4.58: 164 4.58 - 6.87: 21 6.87 - 9.17: 3 9.17 - 11.46: 2 Bond angle restraints: 12519 Sorted by residual: angle pdb=" N PRO C 59 " pdb=" CA PRO C 59 " pdb=" C PRO C 59 " ideal model delta sigma weight residual 113.86 102.40 11.46 1.25e+00 6.40e-01 8.40e+01 angle pdb=" N PHE E 69 " pdb=" CA PHE E 69 " pdb=" C PHE E 69 " ideal model delta sigma weight residual 113.50 107.88 5.62 1.23e+00 6.61e-01 2.09e+01 angle pdb=" C PHE A 235 " pdb=" N ASP A 236 " pdb=" CA ASP A 236 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 angle pdb=" CA ASP E 72 " pdb=" C ASP E 72 " pdb=" O ASP E 72 " ideal model delta sigma weight residual 121.66 117.03 4.63 1.17e+00 7.31e-01 1.56e+01 angle pdb=" C GLN A 120 " pdb=" N SER A 121 " pdb=" CA SER A 121 " ideal model delta sigma weight residual 121.54 128.69 -7.15 1.91e+00 2.74e-01 1.40e+01 ... (remaining 12514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5055 17.82 - 35.64: 406 35.64 - 53.46: 75 53.46 - 71.28: 11 71.28 - 89.10: 5 Dihedral angle restraints: 5552 sinusoidal: 2223 harmonic: 3329 Sorted by residual: dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N GLN A 122 " pdb=" CA GLN A 122 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ALA A 158 " pdb=" C ALA A 158 " pdb=" N ARG A 159 " pdb=" CA ARG A 159 " ideal model delta harmonic sigma weight residual 180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ASN A 542 " pdb=" C ASN A 542 " pdb=" N LYS A 543 " pdb=" CA LYS A 543 " ideal model delta harmonic sigma weight residual -180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 5549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 927 0.035 - 0.069: 294 0.069 - 0.104: 96 0.104 - 0.138: 35 0.138 - 0.173: 5 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CA GLN A 122 " pdb=" N GLN A 122 " pdb=" C GLN A 122 " pdb=" CB GLN A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA ALA C 60 " pdb=" N ALA C 60 " pdb=" C ALA C 60 " pdb=" CB ALA C 60 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CB ILE D 29 " pdb=" CA ILE D 29 " pdb=" CG1 ILE D 29 " pdb=" CG2 ILE D 29 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 1354 not shown) Planarity restraints: 1641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 586 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 587 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 587 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 587 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 139 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO D 140 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 140 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 140 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 57 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C ARG C 57 " 0.022 2.00e-02 2.50e+03 pdb=" O ARG C 57 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU C 58 " -0.007 2.00e-02 2.50e+03 ... (remaining 1638 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1067 2.75 - 3.29: 9347 3.29 - 3.82: 14355 3.82 - 4.36: 15696 4.36 - 4.90: 26954 Nonbonded interactions: 67419 Sorted by model distance: nonbonded pdb=" OG1 THR A 465 " pdb=" O ASP A 495 " model vdw 2.212 3.040 nonbonded pdb=" O ARG A 266 " pdb=" OG1 THR A 334 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 394 " pdb=" O ASP A 447 " model vdw 2.239 3.040 nonbonded pdb=" O SER A 121 " pdb=" N TYR A 123 " model vdw 2.264 3.120 nonbonded pdb=" OG SER A 461 " pdb=" OD1 ASN A 468 " model vdw 2.268 3.040 ... (remaining 67414 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.003 0.043 9253 Z= 0.147 Angle : 0.657 11.458 12519 Z= 0.394 Chirality : 0.041 0.173 1357 Planarity : 0.003 0.040 1641 Dihedral : 13.280 89.099 3430 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.48 % Favored : 89.17 % Rotamer: Outliers : 0.21 % Allowed : 4.83 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.79 (0.22), residues: 1145 helix: -0.61 (0.26), residues: 306 sheet: -2.36 (0.29), residues: 294 loop : -3.84 (0.22), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 366 TYR 0.020 0.001 TYR A 296 PHE 0.019 0.001 PHE A 235 TRP 0.012 0.001 TRP A 267 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9253) covalent geometry : angle 0.65727 (12519) hydrogen bonds : bond 0.20736 ( 321) hydrogen bonds : angle 8.46208 ( 918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8571 (p0) cc_final: 0.8351 (t0) REVERT: A 137 LYS cc_start: 0.9621 (tmtt) cc_final: 0.9395 (tppt) REVERT: A 224 LYS cc_start: 0.9081 (mtpp) cc_final: 0.8697 (ttpp) REVERT: A 435 ASP cc_start: 0.8165 (p0) cc_final: 0.7949 (p0) REVERT: A 619 PHE cc_start: 0.7291 (m-80) cc_final: 0.6422 (m-10) REVERT: C 37 ARG cc_start: 0.8705 (tpp80) cc_final: 0.8406 (tpp80) REVERT: D 96 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7734 (tm-30) REVERT: D 109 ASP cc_start: 0.8704 (p0) cc_final: 0.8184 (p0) REVERT: D 130 LEU cc_start: 0.6598 (tp) cc_final: 0.6341 (tp) REVERT: D 182 MET cc_start: 0.9072 (tpp) cc_final: 0.8723 (tpp) REVERT: E 70 HIS cc_start: 0.7353 (m-70) cc_final: 0.7145 (m-70) outliers start: 2 outliers final: 1 residues processed: 227 average time/residue: 0.0788 time to fit residues: 24.2270 Evaluate side-chains 166 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 260 HIS A 505 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.128352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.095971 restraints weight = 20808.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095019 restraints weight = 18999.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.095669 restraints weight = 19595.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098191 restraints weight = 13517.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098223 restraints weight = 9714.879| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9253 Z= 0.172 Angle : 0.687 9.178 12519 Z= 0.355 Chirality : 0.044 0.211 1357 Planarity : 0.005 0.052 1641 Dihedral : 4.823 31.749 1279 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.18 % Favored : 88.65 % Rotamer: Outliers : 2.00 % Allowed : 14.08 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.16 (0.23), residues: 1145 helix: 0.28 (0.28), residues: 321 sheet: -2.16 (0.28), residues: 306 loop : -3.71 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 660 TYR 0.025 0.002 TYR A 296 PHE 0.021 0.002 PHE A 235 TRP 0.012 0.001 TRP A 295 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9253) covalent geometry : angle 0.68663 (12519) hydrogen bonds : bond 0.03897 ( 321) hydrogen bonds : angle 5.72043 ( 918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 PHE cc_start: 0.8711 (m-10) cc_final: 0.8492 (m-80) REVERT: A 162 VAL cc_start: 0.9460 (m) cc_final: 0.9171 (p) REVERT: A 224 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8645 (ttpt) REVERT: A 237 PHE cc_start: 0.7031 (t80) cc_final: 0.6724 (t80) REVERT: A 267 TRP cc_start: 0.2772 (OUTLIER) cc_final: 0.2291 (m-10) REVERT: A 506 TYR cc_start: 0.9171 (p90) cc_final: 0.8654 (p90) REVERT: C 37 ARG cc_start: 0.8801 (tpp80) cc_final: 0.8513 (tpp80) REVERT: C 41 LEU cc_start: 0.8815 (mt) cc_final: 0.8397 (mt) REVERT: C 51 ASP cc_start: 0.8550 (t0) cc_final: 0.8080 (t0) REVERT: D 51 TYR cc_start: 0.8092 (m-80) cc_final: 0.7851 (m-80) REVERT: D 96 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7836 (tm-30) REVERT: D 109 ASP cc_start: 0.8603 (p0) cc_final: 0.7886 (p0) REVERT: D 123 ASP cc_start: 0.7771 (t70) cc_final: 0.7471 (t70) outliers start: 19 outliers final: 16 residues processed: 181 average time/residue: 0.0785 time to fit residues: 20.1970 Evaluate side-chains 165 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 94 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 22 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 34 optimal weight: 0.1980 chunk 80 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN A 731 ASN C 52 GLN C 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.130150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.097557 restraints weight = 20656.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096652 restraints weight = 18351.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097592 restraints weight = 17267.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099749 restraints weight = 12165.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099764 restraints weight = 9630.214| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9253 Z= 0.124 Angle : 0.647 10.046 12519 Z= 0.331 Chirality : 0.043 0.207 1357 Planarity : 0.004 0.047 1641 Dihedral : 4.770 31.807 1279 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.39 % Favored : 89.43 % Rotamer: Outliers : 2.31 % Allowed : 17.23 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.24), residues: 1145 helix: 0.76 (0.29), residues: 319 sheet: -1.87 (0.29), residues: 305 loop : -3.46 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 34 TYR 0.018 0.001 TYR A 296 PHE 0.014 0.001 PHE A 228 TRP 0.007 0.001 TRP A 295 HIS 0.002 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9253) covalent geometry : angle 0.64696 (12519) hydrogen bonds : bond 0.03231 ( 321) hydrogen bonds : angle 5.08208 ( 918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 VAL cc_start: 0.9419 (m) cc_final: 0.9084 (p) REVERT: A 223 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8741 (mm-30) REVERT: A 224 LYS cc_start: 0.9084 (mtpp) cc_final: 0.8617 (ttpt) REVERT: A 267 TRP cc_start: 0.2757 (OUTLIER) cc_final: 0.2346 (m-10) REVERT: A 351 GLU cc_start: 0.8431 (tp30) cc_final: 0.7771 (tp30) REVERT: A 506 TYR cc_start: 0.9097 (p90) cc_final: 0.8584 (p90) REVERT: A 619 PHE cc_start: 0.7627 (m-80) cc_final: 0.6655 (m-10) REVERT: C 32 GLN cc_start: 0.8030 (tp40) cc_final: 0.7667 (mp10) REVERT: C 37 ARG cc_start: 0.8819 (tpp80) cc_final: 0.8586 (tpp80) REVERT: C 41 LEU cc_start: 0.8718 (mt) cc_final: 0.8383 (mt) REVERT: C 52 GLN cc_start: 0.8275 (mp-120) cc_final: 0.8009 (mp10) REVERT: D 96 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7818 (tm-30) REVERT: D 109 ASP cc_start: 0.8575 (p0) cc_final: 0.7813 (p0) REVERT: D 123 ASP cc_start: 0.7772 (t70) cc_final: 0.7425 (t70) REVERT: D 130 LEU cc_start: 0.6732 (tp) cc_final: 0.6380 (tp) REVERT: E 97 GLU cc_start: 0.7963 (pm20) cc_final: 0.7693 (pm20) outliers start: 22 outliers final: 13 residues processed: 190 average time/residue: 0.0754 time to fit residues: 20.4250 Evaluate side-chains 163 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN D 133 GLN E 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.133860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.102397 restraints weight = 20154.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.101724 restraints weight = 15581.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102816 restraints weight = 16218.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103135 restraints weight = 11112.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.103618 restraints weight = 10075.384| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9253 Z= 0.114 Angle : 0.652 10.770 12519 Z= 0.327 Chirality : 0.042 0.204 1357 Planarity : 0.004 0.048 1641 Dihedral : 4.675 31.646 1279 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.57 % Favored : 89.26 % Rotamer: Outliers : 2.21 % Allowed : 20.27 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.24), residues: 1145 helix: 0.85 (0.29), residues: 321 sheet: -1.58 (0.29), residues: 305 loop : -3.27 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 660 TYR 0.023 0.001 TYR D 58 PHE 0.016 0.001 PHE D 98 TRP 0.006 0.001 TRP A 295 HIS 0.002 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9253) covalent geometry : angle 0.65197 (12519) hydrogen bonds : bond 0.03004 ( 321) hydrogen bonds : angle 4.82989 ( 918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 VAL cc_start: 0.9347 (m) cc_final: 0.9018 (p) REVERT: A 168 ILE cc_start: 0.8534 (mp) cc_final: 0.8272 (mm) REVERT: A 224 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8603 (ttpt) REVERT: A 506 TYR cc_start: 0.9025 (p90) cc_final: 0.8612 (p90) REVERT: C 32 GLN cc_start: 0.8044 (tp40) cc_final: 0.7666 (mp10) REVERT: C 37 ARG cc_start: 0.8745 (tpp80) cc_final: 0.8520 (tpp80) REVERT: C 73 ARG cc_start: 0.8214 (mpp80) cc_final: 0.7395 (mpp80) REVERT: D 51 TYR cc_start: 0.7782 (m-10) cc_final: 0.7471 (m-80) REVERT: D 96 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7688 (tm-30) REVERT: D 109 ASP cc_start: 0.8556 (p0) cc_final: 0.7768 (p0) REVERT: D 123 ASP cc_start: 0.7813 (t70) cc_final: 0.7461 (t70) REVERT: D 130 LEU cc_start: 0.6711 (tp) cc_final: 0.6465 (tp) REVERT: E 97 GLU cc_start: 0.7812 (pm20) cc_final: 0.7515 (pm20) outliers start: 21 outliers final: 16 residues processed: 183 average time/residue: 0.0738 time to fit residues: 19.5434 Evaluate side-chains 167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 94 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN E 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.099248 restraints weight = 20382.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099164 restraints weight = 16551.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.099968 restraints weight = 15739.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.100584 restraints weight = 11084.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100990 restraints weight = 10028.470| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9253 Z= 0.137 Angle : 0.670 10.573 12519 Z= 0.335 Chirality : 0.042 0.201 1357 Planarity : 0.004 0.044 1641 Dihedral : 4.670 26.849 1277 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.00 % Favored : 88.82 % Rotamer: Outliers : 3.05 % Allowed : 20.69 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.25), residues: 1145 helix: 0.92 (0.29), residues: 322 sheet: -1.40 (0.30), residues: 302 loop : -3.18 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 74 TYR 0.041 0.001 TYR D 58 PHE 0.018 0.001 PHE D 98 TRP 0.019 0.001 TRP A 267 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9253) covalent geometry : angle 0.66968 (12519) hydrogen bonds : bond 0.03109 ( 321) hydrogen bonds : angle 4.79258 ( 918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LYS cc_start: 0.9070 (mtpp) cc_final: 0.8670 (ttpt) REVERT: A 362 ASP cc_start: 0.8563 (t70) cc_final: 0.8154 (t0) REVERT: A 506 TYR cc_start: 0.9052 (p90) cc_final: 0.8620 (p90) REVERT: C 37 ARG cc_start: 0.8774 (tpp80) cc_final: 0.8514 (tpp80) REVERT: C 41 LEU cc_start: 0.8718 (mt) cc_final: 0.8414 (mt) REVERT: D 51 TYR cc_start: 0.7876 (m-10) cc_final: 0.7473 (m-80) REVERT: D 96 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7770 (tm-30) REVERT: D 109 ASP cc_start: 0.8589 (p0) cc_final: 0.7838 (p0) REVERT: D 123 ASP cc_start: 0.7904 (t70) cc_final: 0.7585 (t70) REVERT: D 130 LEU cc_start: 0.6855 (tp) cc_final: 0.6577 (tp) REVERT: E 97 GLU cc_start: 0.7788 (pm20) cc_final: 0.7462 (pm20) outliers start: 29 outliers final: 20 residues processed: 179 average time/residue: 0.0726 time to fit residues: 18.8217 Evaluate side-chains 168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 94 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.0020 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 415 ASN C 52 GLN C 79 GLN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.095786 restraints weight = 20473.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.095325 restraints weight = 17907.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096195 restraints weight = 19329.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.096527 restraints weight = 12459.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097189 restraints weight = 11238.925| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9253 Z= 0.195 Angle : 0.709 9.784 12519 Z= 0.359 Chirality : 0.044 0.211 1357 Planarity : 0.004 0.047 1641 Dihedral : 5.003 27.507 1277 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.19 % Favored : 86.64 % Rotamer: Outliers : 3.78 % Allowed : 21.32 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.25), residues: 1145 helix: 0.87 (0.28), residues: 319 sheet: -1.43 (0.30), residues: 305 loop : -3.18 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 660 TYR 0.030 0.002 TYR D 58 PHE 0.022 0.002 PHE D 98 TRP 0.009 0.001 TRP A 267 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9253) covalent geometry : angle 0.70937 (12519) hydrogen bonds : bond 0.03493 ( 321) hydrogen bonds : angle 4.96196 ( 918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: A 224 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8532 (ttpt) REVERT: A 357 ASN cc_start: 0.8436 (t0) cc_final: 0.8067 (t0) REVERT: A 362 ASP cc_start: 0.8548 (t70) cc_final: 0.8167 (t0) REVERT: A 506 TYR cc_start: 0.9105 (p90) cc_final: 0.8798 (p90) REVERT: C 37 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8564 (tpp80) REVERT: C 41 LEU cc_start: 0.8841 (mt) cc_final: 0.8558 (mt) REVERT: C 80 GLN cc_start: 0.6357 (mp10) cc_final: 0.6069 (mp10) REVERT: D 51 TYR cc_start: 0.7867 (m-10) cc_final: 0.7477 (m-10) REVERT: D 55 VAL cc_start: 0.8963 (m) cc_final: 0.8730 (p) REVERT: D 96 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7730 (tm-30) REVERT: D 109 ASP cc_start: 0.8629 (p0) cc_final: 0.7787 (p0) REVERT: D 123 ASP cc_start: 0.7802 (t70) cc_final: 0.7521 (t70) REVERT: D 130 LEU cc_start: 0.7148 (tp) cc_final: 0.6778 (tp) REVERT: D 137 ASP cc_start: 0.8283 (p0) cc_final: 0.7625 (p0) REVERT: E 97 GLU cc_start: 0.7710 (pm20) cc_final: 0.7288 (pm20) outliers start: 36 outliers final: 27 residues processed: 176 average time/residue: 0.0722 time to fit residues: 18.4891 Evaluate side-chains 173 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TYR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 116 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 47 optimal weight: 0.1980 chunk 62 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 18 optimal weight: 0.0060 chunk 104 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN E 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098797 restraints weight = 20009.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.099838 restraints weight = 15648.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.100632 restraints weight = 12627.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.101281 restraints weight = 9452.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.101587 restraints weight = 8651.183| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9253 Z= 0.129 Angle : 0.676 10.973 12519 Z= 0.341 Chirality : 0.043 0.213 1357 Planarity : 0.004 0.053 1641 Dihedral : 4.829 27.589 1277 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.92 % Favored : 89.00 % Rotamer: Outliers : 3.05 % Allowed : 23.11 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.25), residues: 1145 helix: 0.95 (0.29), residues: 323 sheet: -1.34 (0.29), residues: 302 loop : -3.14 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 57 TYR 0.021 0.001 TYR D 39 PHE 0.022 0.001 PHE D 98 TRP 0.008 0.001 TRP D 33 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9253) covalent geometry : angle 0.67583 (12519) hydrogen bonds : bond 0.03122 ( 321) hydrogen bonds : angle 4.78451 ( 918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: A 137 LYS cc_start: 0.9653 (tmtt) cc_final: 0.9436 (tptp) REVERT: A 224 LYS cc_start: 0.9027 (mtpp) cc_final: 0.8584 (ttpt) REVERT: A 351 GLU cc_start: 0.8385 (tp30) cc_final: 0.7949 (tp30) REVERT: A 357 ASN cc_start: 0.8302 (t0) cc_final: 0.7904 (t0) REVERT: A 362 ASP cc_start: 0.8547 (t70) cc_final: 0.8151 (t0) REVERT: A 506 TYR cc_start: 0.9080 (p90) cc_final: 0.8765 (p90) REVERT: C 41 LEU cc_start: 0.8850 (mt) cc_final: 0.8544 (mt) REVERT: C 78 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7037 (m) REVERT: C 80 GLN cc_start: 0.6370 (mp10) cc_final: 0.6116 (mp10) REVERT: D 51 TYR cc_start: 0.7803 (m-10) cc_final: 0.7477 (m-10) REVERT: D 96 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7738 (tm-30) REVERT: D 109 ASP cc_start: 0.8577 (p0) cc_final: 0.7846 (p0) REVERT: D 123 ASP cc_start: 0.7842 (t70) cc_final: 0.7547 (t70) REVERT: D 130 LEU cc_start: 0.6703 (tp) cc_final: 0.6488 (tp) REVERT: E 97 GLU cc_start: 0.7709 (pm20) cc_final: 0.7282 (pm20) outliers start: 29 outliers final: 25 residues processed: 176 average time/residue: 0.0698 time to fit residues: 17.9567 Evaluate side-chains 171 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TYR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 94 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 86 optimal weight: 10.0000 chunk 75 optimal weight: 0.0030 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 61 optimal weight: 10.0000 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.099066 restraints weight = 19961.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098518 restraints weight = 15736.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099548 restraints weight = 15557.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100115 restraints weight = 10862.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.100461 restraints weight = 9871.692| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9253 Z= 0.138 Angle : 0.691 12.283 12519 Z= 0.346 Chirality : 0.043 0.214 1357 Planarity : 0.004 0.048 1641 Dihedral : 4.759 27.003 1277 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.62 % Favored : 88.30 % Rotamer: Outliers : 3.47 % Allowed : 23.42 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.25), residues: 1145 helix: 0.90 (0.29), residues: 325 sheet: -1.29 (0.30), residues: 302 loop : -3.10 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 57 TYR 0.028 0.001 TYR A 735 PHE 0.023 0.001 PHE D 98 TRP 0.007 0.001 TRP A 267 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9253) covalent geometry : angle 0.69070 (12519) hydrogen bonds : bond 0.03114 ( 321) hydrogen bonds : angle 4.74120 ( 918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: A 137 LYS cc_start: 0.9665 (tmtt) cc_final: 0.9445 (tptp) REVERT: A 224 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8626 (ttpt) REVERT: A 351 GLU cc_start: 0.8365 (tp30) cc_final: 0.7888 (tp30) REVERT: A 357 ASN cc_start: 0.8278 (t0) cc_final: 0.8068 (t0) REVERT: A 362 ASP cc_start: 0.8563 (t70) cc_final: 0.8166 (t0) REVERT: A 506 TYR cc_start: 0.9102 (p90) cc_final: 0.8785 (p90) REVERT: C 41 LEU cc_start: 0.8846 (mt) cc_final: 0.8547 (mt) REVERT: C 78 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7122 (m) REVERT: C 80 GLN cc_start: 0.6334 (mp10) cc_final: 0.6083 (mp10) REVERT: D 51 TYR cc_start: 0.7866 (m-10) cc_final: 0.7580 (m-10) REVERT: D 96 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7783 (tm-30) REVERT: D 109 ASP cc_start: 0.8602 (p0) cc_final: 0.7853 (p0) REVERT: D 130 LEU cc_start: 0.6742 (tp) cc_final: 0.6536 (tp) REVERT: E 97 GLU cc_start: 0.7702 (pm20) cc_final: 0.7357 (pm20) outliers start: 33 outliers final: 29 residues processed: 174 average time/residue: 0.0625 time to fit residues: 15.9861 Evaluate side-chains 176 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TYR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 116 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN D 253 HIS E 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099641 restraints weight = 20340.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.098615 restraints weight = 17724.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.099332 restraints weight = 17740.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.101430 restraints weight = 12603.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.101472 restraints weight = 9572.821| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9253 Z= 0.131 Angle : 0.686 11.583 12519 Z= 0.344 Chirality : 0.042 0.216 1357 Planarity : 0.004 0.046 1641 Dihedral : 4.726 26.858 1277 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.92 % Favored : 89.00 % Rotamer: Outliers : 3.57 % Allowed : 23.53 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.25), residues: 1145 helix: 0.94 (0.29), residues: 324 sheet: -1.21 (0.30), residues: 300 loop : -3.07 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 57 TYR 0.019 0.001 TYR C 31 PHE 0.024 0.001 PHE D 98 TRP 0.009 0.001 TRP A 295 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9253) covalent geometry : angle 0.68575 (12519) hydrogen bonds : bond 0.03071 ( 321) hydrogen bonds : angle 4.64386 ( 918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: A 137 LYS cc_start: 0.9639 (tmtt) cc_final: 0.9431 (tptp) REVERT: A 224 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8728 (ttpt) REVERT: A 351 GLU cc_start: 0.8362 (tp30) cc_final: 0.7986 (tp30) REVERT: A 357 ASN cc_start: 0.8303 (t0) cc_final: 0.7923 (t0) REVERT: A 362 ASP cc_start: 0.8544 (t70) cc_final: 0.8151 (t0) REVERT: A 506 TYR cc_start: 0.9098 (p90) cc_final: 0.8781 (p90) REVERT: C 41 LEU cc_start: 0.8845 (mt) cc_final: 0.8532 (mt) REVERT: C 78 VAL cc_start: 0.7454 (OUTLIER) cc_final: 0.7192 (m) REVERT: C 80 GLN cc_start: 0.6357 (mp10) cc_final: 0.6133 (mp10) REVERT: D 51 TYR cc_start: 0.7787 (m-10) cc_final: 0.7493 (m-10) REVERT: D 96 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7773 (tm-30) REVERT: D 109 ASP cc_start: 0.8589 (p0) cc_final: 0.7830 (p0) REVERT: E 97 GLU cc_start: 0.7639 (pm20) cc_final: 0.7273 (pm20) outliers start: 34 outliers final: 30 residues processed: 181 average time/residue: 0.0668 time to fit residues: 17.8416 Evaluate side-chains 181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TYR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 116 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 8 optimal weight: 0.0020 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098129 restraints weight = 19980.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098039 restraints weight = 12925.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098271 restraints weight = 10390.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098946 restraints weight = 9900.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098983 restraints weight = 8897.796| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9253 Z= 0.121 Angle : 0.701 11.456 12519 Z= 0.348 Chirality : 0.043 0.215 1357 Planarity : 0.004 0.044 1641 Dihedral : 4.655 26.781 1277 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.92 % Favored : 89.00 % Rotamer: Outliers : 2.73 % Allowed : 24.47 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.25), residues: 1145 helix: 0.92 (0.29), residues: 324 sheet: -1.11 (0.30), residues: 299 loop : -3.01 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 57 TYR 0.020 0.001 TYR C 31 PHE 0.024 0.001 PHE D 98 TRP 0.009 0.001 TRP A 267 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9253) covalent geometry : angle 0.70124 (12519) hydrogen bonds : bond 0.02985 ( 321) hydrogen bonds : angle 4.56685 ( 918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: A 137 LYS cc_start: 0.9641 (tmtt) cc_final: 0.9428 (tptp) REVERT: A 224 LYS cc_start: 0.9186 (mtpp) cc_final: 0.8813 (ttpt) REVERT: A 351 GLU cc_start: 0.8229 (tp30) cc_final: 0.7763 (tp30) REVERT: A 357 ASN cc_start: 0.8278 (t0) cc_final: 0.7949 (t0) REVERT: A 362 ASP cc_start: 0.8564 (t70) cc_final: 0.8234 (t0) REVERT: A 506 TYR cc_start: 0.9121 (p90) cc_final: 0.8804 (p90) REVERT: A 716 SER cc_start: 0.8163 (p) cc_final: 0.7912 (p) REVERT: C 41 LEU cc_start: 0.8810 (mt) cc_final: 0.8527 (mt) REVERT: C 78 VAL cc_start: 0.7406 (OUTLIER) cc_final: 0.7137 (m) REVERT: C 80 GLN cc_start: 0.6382 (mp10) cc_final: 0.6110 (mp10) REVERT: D 51 TYR cc_start: 0.7897 (m-10) cc_final: 0.7626 (m-10) REVERT: D 96 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7826 (tm-30) REVERT: E 97 GLU cc_start: 0.7733 (pm20) cc_final: 0.7298 (pm20) outliers start: 26 outliers final: 23 residues processed: 176 average time/residue: 0.0645 time to fit residues: 16.6867 Evaluate side-chains 178 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TYR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 771 TYR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 116 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.126964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094966 restraints weight = 20136.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094386 restraints weight = 16975.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095163 restraints weight = 17540.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.095878 restraints weight = 11798.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096563 restraints weight = 10472.415| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9253 Z= 0.186 Angle : 0.755 12.024 12519 Z= 0.377 Chirality : 0.044 0.211 1357 Planarity : 0.004 0.047 1641 Dihedral : 4.882 26.798 1277 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.14 % Favored : 87.77 % Rotamer: Outliers : 3.36 % Allowed : 24.05 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.25), residues: 1145 helix: 0.85 (0.29), residues: 323 sheet: -1.17 (0.30), residues: 303 loop : -3.07 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 57 TYR 0.019 0.002 TYR A 296 PHE 0.026 0.002 PHE D 98 TRP 0.009 0.001 TRP A 267 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9253) covalent geometry : angle 0.75539 (12519) hydrogen bonds : bond 0.03374 ( 321) hydrogen bonds : angle 4.82308 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1245.03 seconds wall clock time: 22 minutes 10.74 seconds (1330.74 seconds total)