Starting phenix.real_space_refine on Fri Sep 11 01:42:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vrh_21368/09_2026/6vrh_21368.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrh_21368/09_2026/6vrh_21368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vrh_21368/09_2026/6vrh_21368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrh_21368/09_2026/6vrh_21368.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vrh_21368/09_2026/6vrh_21368.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vrh_21368/09_2026/6vrh_21368.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vrh_21368/09_2026/6vrh_21368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrh_21368/09_2026/6vrh_21368.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.946 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 92 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 4045 2.51 5 N 958 2.21 5 O 1103 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6142 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4311 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 517} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 924 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 88 Unusual residues: {' CL': 1, '8PR': 1, 'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.78, per 1000 atoms: 0.29 Number of scatterers: 6142 At special positions: 0 Unit cell: (96.552, 103.032, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 F 1 9.00 O 1103 8.00 N 958 7.00 C 4045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 208 " " NAG A 704 " - " ASN A 217 " Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 426.5 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 57.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.752A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 113 through 116 removed outlier: 3.525A pdb=" N ALA A 116 " --> pdb=" O GLY A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 128 through 144 removed outlier: 3.858A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.639A pdb=" N ARG A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 159 through 190 removed outlier: 4.250A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.653A pdb=" N THR A 198 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 199 " --> pdb=" O PRO A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 199' Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.701A pdb=" N ARG A 241 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 271 removed outlier: 3.591A pdb=" N ALA A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 4.155A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.698A pdb=" N ILE A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 removed outlier: 4.354A pdb=" N GLY A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.546A pdb=" N LEU A 321 " --> pdb=" O GLN A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 322 through 338 removed outlier: 4.248A pdb=" N TRP A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.565A pdb=" N TYR A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 390 removed outlier: 3.688A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.631A pdb=" N VAL A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 419 through 454 removed outlier: 3.694A pdb=" N PHE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.657A pdb=" N VAL A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 484 through 496 removed outlier: 3.758A pdb=" N VAL A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 514 Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 543 Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.777A pdb=" N SER A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 587 removed outlier: 4.045A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.546A pdb=" N TYR A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 612 removed outlier: 3.740A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.931A pdb=" N TYR B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.877A pdb=" N LYS B 84 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.553A pdb=" N THR C 89 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 11.180A pdb=" N GLN C 47 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N SER C 87 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 12.093A pdb=" N VAL C 49 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 11.818A pdb=" N SER C 85 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 73 through 74 removed outlier: 6.052A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 68 " --> pdb=" O TRP C 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.732A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR B 127 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.732A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 897 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: 0.99 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1812 1.34 - 1.46: 1621 1.46 - 1.58: 2844 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6326 Sorted by residual: bond pdb=" CAT 8PR A 702 " pdb=" CAX 8PR A 702 " ideal model delta sigma weight residual 1.509 1.570 -0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" CAV 8PR A 702 " pdb=" OAQ 8PR A 702 " ideal model delta sigma weight residual 1.354 1.413 -0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" CAI 8PR A 702 " pdb=" NAN 8PR A 702 " ideal model delta sigma weight residual 1.452 1.504 -0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" CAU 8PR A 702 " pdb=" OAP 8PR A 702 " ideal model delta sigma weight residual 1.362 1.413 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" CAK 8PR A 702 " pdb=" NAN 8PR A 702 " ideal model delta sigma weight residual 1.451 1.498 -0.047 2.00e-02 2.50e+03 5.56e+00 ... (remaining 6321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 8515 2.20 - 4.40: 80 4.40 - 6.60: 16 6.60 - 8.80: 6 8.80 - 11.00: 2 Bond angle restraints: 8619 Sorted by residual: angle pdb=" CAE 8PR A 702 " pdb=" CAT 8PR A 702 " pdb=" CAX 8PR A 702 " ideal model delta sigma weight residual 120.67 109.67 11.00 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N ARG B 121 " pdb=" CA ARG B 121 " pdb=" C ARG B 121 " ideal model delta sigma weight residual 109.81 117.41 -7.60 2.21e+00 2.05e-01 1.18e+01 angle pdb=" C2 LMT A 705 " pdb=" C3 LMT A 705 " pdb=" C4 LMT A 705 " ideal model delta sigma weight residual 117.09 107.26 9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CAF 8PR A 702 " pdb=" CAT 8PR A 702 " pdb=" CAX 8PR A 702 " ideal model delta sigma weight residual 121.28 130.08 -8.80 3.00e+00 1.11e-01 8.60e+00 angle pdb=" C10 LMT A 705 " pdb=" C9 LMT A 705 " pdb=" C8 LMT A 705 " ideal model delta sigma weight residual 116.03 107.37 8.66 3.00e+00 1.11e-01 8.33e+00 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3249 17.96 - 35.92: 287 35.92 - 53.88: 39 53.88 - 71.83: 3 71.83 - 89.79: 2 Dihedral angle restraints: 3580 sinusoidal: 1366 harmonic: 2214 Sorted by residual: dihedral pdb=" CA ARG B 121 " pdb=" C ARG B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta harmonic sigma weight residual 180.00 129.71 50.29 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CB GLU A 78 " pdb=" CG GLU A 78 " pdb=" CD GLU A 78 " pdb=" OE1 GLU A 78 " ideal model delta sinusoidal sigma weight residual 0.00 89.79 -89.79 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA THR A 497 " pdb=" C THR A 497 " pdb=" N GLY A 498 " pdb=" CA GLY A 498 " ideal model delta harmonic sigma weight residual -180.00 -165.11 -14.89 0 5.00e+00 4.00e-02 8.86e+00 ... (remaining 3577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 727 0.043 - 0.085: 193 0.085 - 0.128: 41 0.128 - 0.171: 1 0.171 - 0.213: 4 Chirality restraints: 966 Sorted by residual: chirality pdb=" C5' LMT A 705 " pdb=" C4' LMT A 705 " pdb=" C6' LMT A 705 " pdb=" O5' LMT A 705 " both_signs ideal model delta sigma weight residual False -2.51 -2.29 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C4' LMT A 705 " pdb=" C3' LMT A 705 " pdb=" C5' LMT A 705 " pdb=" O1B LMT A 705 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CAX 8PR A 702 " pdb=" CAJ 8PR A 702 " pdb=" CAT 8PR A 702 " pdb=" CAW 8PR A 702 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 963 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 121 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO B 122 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.21e+00 pdb=" N PRO A 288 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 130 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A 131 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.015 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 743 2.75 - 3.29: 6254 3.29 - 3.82: 10369 3.82 - 4.36: 11887 4.36 - 4.90: 20868 Nonbonded interactions: 50121 Sorted by model distance: nonbonded pdb=" O PRO A 571 " pdb=" OG SER A 574 " model vdw 2.212 3.040 nonbonded pdb=" OG SER A 242 " pdb=" O LEU A 248 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR C 56 " pdb=" OE1 GLN C 109 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP A 328 " pdb=" O4' LMT A 705 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR C 83 " pdb=" OG1 THR C 94 " model vdw 2.307 3.040 ... (remaining 50116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.060 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 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 : 0.004 0.061 6331 Z= 0.181 Angle : 0.604 11.004 8631 Z= 0.292 Chirality : 0.040 0.213 966 Planarity : 0.004 0.073 1048 Dihedral : 12.994 89.792 2165 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -3.01 (0.27), residues: 758 helix: -1.15 (0.24), residues: 360 sheet: -2.83 (0.43), residues: 105 loop : -2.61 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 390 TYR 0.014 0.001 TYR B 123 PHE 0.013 0.001 PHE A 380 TRP 0.008 0.001 TRP A 197 HIS 0.006 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 ( 6326) covalent geometry : angle 0.60374 / 0.29 ( 8619) SS BOND : bond 0.00314 / 0.17 ( 3) SS BOND : angle 0.37720 / 0.21 ( 6) hydrogen bonds : bond 0.17441 / 11.47 ( 306) hydrogen bonds : angle 6.90517 / 5.14 ( 897) link_NAG-ASN : bond 0.00175 / 0.10 ( 2) link_NAG-ASN : angle 0.78022 / 0.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.7829 (t80) cc_final: 0.7608 (t80) REVERT: A 270 ILE cc_start: 0.7191 (tp) cc_final: 0.6813 (tp) REVERT: A 271 TRP cc_start: 0.5986 (p-90) cc_final: 0.5554 (p-90) REVERT: A 272 LYS cc_start: 0.8402 (tppp) cc_final: 0.7912 (tptt) REVERT: A 311 PHE cc_start: 0.6600 (m-10) cc_final: 0.6390 (m-80) REVERT: A 316 ASN cc_start: 0.7477 (t0) cc_final: 0.6859 (t0) REVERT: A 615 GLU cc_start: 0.5133 (mp0) cc_final: 0.3315 (pt0) REVERT: C 62 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6364 (mt0) REVERT: C 73 TYR cc_start: 0.8083 (m-80) cc_final: 0.7785 (m-80) REVERT: C 81 ARG cc_start: 0.6620 (tpm170) cc_final: 0.4840 (ptt90) REVERT: C 123 LYS cc_start: 0.6894 (mptt) cc_final: 0.6315 (mtpt) REVERT: B 39 ILE cc_start: 0.6117 (mm) cc_final: 0.5845 (tp) REVERT: B 57 LYS cc_start: 0.7771 (tttt) cc_final: 0.7131 (tttt) REVERT: B 130 GLN cc_start: 0.7601 (pt0) cc_final: 0.7401 (pt0) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0766 time to fit residues: 11.3455 Evaluate side-chains 91 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 111 GLN A 112 ASN A 235 HIS C 26 GLN C 47 GLN C 57 GLN B 54 ASN B 69 ASN B 130 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.197097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.176638 restraints weight = 8037.017| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.89 r_work: 0.3933 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6331 Z= 0.147 Angle : 0.558 8.661 8631 Z= 0.288 Chirality : 0.040 0.132 966 Planarity : 0.004 0.079 1048 Dihedral : 5.062 52.104 849 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.69 % Allowed : 11.38 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.56 (0.30), residues: 758 helix: 0.17 (0.26), residues: 370 sheet: -2.18 (0.44), residues: 106 loop : -2.11 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.035 0.002 TYR A 142 PHE 0.017 0.001 PHE A 548 TRP 0.022 0.001 TRP A 103 HIS 0.010 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 6326) covalent geometry : angle 0.55748 / 0.29 ( 8619) SS BOND : bond 0.00112 / 0.07 ( 3) SS BOND : angle 0.43995 / 0.26 ( 6) hydrogen bonds : bond 0.03929 / 2.55 ( 306) hydrogen bonds : angle 4.72214 / 3.48 ( 897) link_NAG-ASN : bond 0.00295 / 0.16 ( 2) link_NAG-ASN : angle 1.04038 / 0.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.8244 (t80) cc_final: 0.7945 (t80) REVERT: A 204 TRP cc_start: 0.6908 (p90) cc_final: 0.6320 (p90) REVERT: A 270 ILE cc_start: 0.7062 (tp) cc_final: 0.6713 (tp) REVERT: A 271 TRP cc_start: 0.5883 (p-90) cc_final: 0.5398 (p-90) REVERT: A 272 LYS cc_start: 0.8592 (tppp) cc_final: 0.8105 (tptp) REVERT: A 316 ASN cc_start: 0.7594 (t0) cc_final: 0.6941 (t0) REVERT: A 615 GLU cc_start: 0.5276 (mp0) cc_final: 0.3189 (pt0) REVERT: C 56 TYR cc_start: 0.8719 (m-80) cc_final: 0.8287 (m-80) REVERT: C 62 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6525 (mt0) REVERT: C 81 ARG cc_start: 0.6934 (tpm170) cc_final: 0.5146 (ptt90) REVERT: C 123 LYS cc_start: 0.7175 (mptt) cc_final: 0.6460 (mtpt) outliers start: 11 outliers final: 9 residues processed: 88 average time/residue: 0.0652 time to fit residues: 7.9001 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.199582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.178905 restraints weight = 7954.704| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.89 r_work: 0.3953 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6331 Z= 0.111 Angle : 0.524 7.677 8631 Z= 0.271 Chirality : 0.039 0.129 966 Planarity : 0.004 0.077 1048 Dihedral : 4.892 52.782 849 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.46 % Allowed : 12.31 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.90 (0.31), residues: 758 helix: 0.72 (0.27), residues: 371 sheet: -1.70 (0.46), residues: 106 loop : -1.90 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.021 0.001 TYR A 142 PHE 0.029 0.001 PHE A 311 TRP 0.013 0.001 TRP A 103 HIS 0.008 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6326) covalent geometry : angle 0.52382 / 0.27 ( 8619) SS BOND : bond 0.00198 / 0.12 ( 3) SS BOND : angle 0.46329 / 0.25 ( 6) hydrogen bonds : bond 0.03560 / 2.31 ( 306) hydrogen bonds : angle 4.36972 / 3.25 ( 897) link_NAG-ASN : bond 0.00217 / 0.13 ( 2) link_NAG-ASN : angle 0.88227 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 204 TRP cc_start: 0.6855 (p90) cc_final: 0.6248 (p90) REVERT: A 270 ILE cc_start: 0.7033 (tp) cc_final: 0.6672 (tp) REVERT: A 316 ASN cc_start: 0.7582 (t0) cc_final: 0.6901 (t0) REVERT: A 507 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6894 (tt) REVERT: A 606 GLU cc_start: 0.6334 (tt0) cc_final: 0.6099 (tt0) REVERT: A 615 GLU cc_start: 0.5254 (mp0) cc_final: 0.3197 (pt0) REVERT: C 56 TYR cc_start: 0.8701 (m-80) cc_final: 0.8269 (m-80) REVERT: C 62 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6572 (mt0) REVERT: C 81 ARG cc_start: 0.7057 (tpm170) cc_final: 0.5216 (ptt90) REVERT: C 123 LYS cc_start: 0.7152 (mptt) cc_final: 0.6414 (tttm) outliers start: 16 outliers final: 10 residues processed: 89 average time/residue: 0.0710 time to fit residues: 8.6361 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 0.0980 chunk 2 optimal weight: 0.0040 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN C 26 GLN B 54 ASN B 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.201844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.181241 restraints weight = 7978.544| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.89 r_work: 0.3973 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6331 Z= 0.100 Angle : 0.500 7.687 8631 Z= 0.260 Chirality : 0.038 0.124 966 Planarity : 0.004 0.076 1048 Dihedral : 4.710 51.449 849 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.31 % Allowed : 14.77 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.46 (0.31), residues: 758 helix: 0.99 (0.27), residues: 373 sheet: -1.26 (0.47), residues: 106 loop : -1.66 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.020 0.001 TYR A 134 PHE 0.044 0.001 PHE A 311 TRP 0.011 0.001 TRP B 55 HIS 0.007 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 6326) covalent geometry : angle 0.49954 / 0.26 ( 8619) SS BOND : bond 0.00143 / 0.07 ( 3) SS BOND : angle 0.30239 / 0.16 ( 6) hydrogen bonds : bond 0.03269 / 2.12 ( 306) hydrogen bonds : angle 4.19684 / 3.14 ( 897) link_NAG-ASN : bond 0.00211 / 0.12 ( 2) link_NAG-ASN : angle 0.88305 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 204 TRP cc_start: 0.6780 (p90) cc_final: 0.6139 (p90) REVERT: A 270 ILE cc_start: 0.6998 (tp) cc_final: 0.6653 (tp) REVERT: A 271 TRP cc_start: 0.5936 (p-90) cc_final: 0.5476 (p-90) REVERT: A 316 ASN cc_start: 0.7527 (t0) cc_final: 0.6823 (t0) REVERT: A 606 GLU cc_start: 0.6246 (tt0) cc_final: 0.5978 (tt0) REVERT: A 615 GLU cc_start: 0.5261 (mp0) cc_final: 0.3240 (pt0) REVERT: C 31 MET cc_start: 0.1858 (mtm) cc_final: 0.1577 (mpp) REVERT: C 62 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6564 (mt0) REVERT: C 73 TYR cc_start: 0.8028 (m-80) cc_final: 0.7794 (m-80) REVERT: C 81 ARG cc_start: 0.7054 (tpm170) cc_final: 0.5254 (ptt90) REVERT: C 123 LYS cc_start: 0.7120 (mptt) cc_final: 0.6385 (tttm) outliers start: 15 outliers final: 13 residues processed: 85 average time/residue: 0.0661 time to fit residues: 7.7173 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 0.0020 chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.201287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.179990 restraints weight = 8127.496| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 3.07 r_work: 0.3958 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6331 Z= 0.110 Angle : 0.508 8.223 8631 Z= 0.260 Chirality : 0.038 0.127 966 Planarity : 0.004 0.076 1048 Dihedral : 4.696 50.743 849 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.31 % Allowed : 15.38 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.32 (0.31), residues: 758 helix: 1.04 (0.27), residues: 375 sheet: -1.17 (0.48), residues: 106 loop : -1.53 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.024 0.001 TYR A 134 PHE 0.036 0.001 PHE A 311 TRP 0.008 0.001 TRP A 103 HIS 0.007 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 6326) covalent geometry : angle 0.50725 / 0.26 ( 8619) SS BOND : bond 0.00152 / 0.08 ( 3) SS BOND : angle 0.44956 / 0.25 ( 6) hydrogen bonds : bond 0.03302 / 2.14 ( 306) hydrogen bonds : angle 4.16869 / 3.12 ( 897) link_NAG-ASN : bond 0.00199 / 0.11 ( 2) link_NAG-ASN : angle 0.86022 / 0.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.7433 (mmp) cc_final: 0.7100 (mmp) REVERT: A 135 MET cc_start: 0.8690 (ttp) cc_final: 0.8393 (ttp) REVERT: A 176 TYR cc_start: 0.8111 (t80) cc_final: 0.7885 (t80) REVERT: A 204 TRP cc_start: 0.6738 (p90) cc_final: 0.6137 (p90) REVERT: A 270 ILE cc_start: 0.6879 (tp) cc_final: 0.6545 (tp) REVERT: A 271 TRP cc_start: 0.5782 (p-90) cc_final: 0.5342 (p-90) REVERT: A 311 PHE cc_start: 0.7040 (m-80) cc_final: 0.6818 (m-80) REVERT: A 316 ASN cc_start: 0.7340 (t0) cc_final: 0.6618 (t0) REVERT: A 507 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6846 (tt) REVERT: A 606 GLU cc_start: 0.6303 (tt0) cc_final: 0.6018 (tt0) REVERT: A 615 GLU cc_start: 0.5252 (mp0) cc_final: 0.3173 (pt0) REVERT: C 31 MET cc_start: 0.1785 (mtm) cc_final: 0.1497 (mpp) REVERT: C 62 GLN cc_start: 0.6934 (mm-40) cc_final: 0.6422 (mt0) REVERT: C 81 ARG cc_start: 0.7017 (tpm170) cc_final: 0.5152 (ptt90) REVERT: C 123 LYS cc_start: 0.7136 (mptt) cc_final: 0.6374 (tttm) outliers start: 15 outliers final: 12 residues processed: 81 average time/residue: 0.0759 time to fit residues: 8.4121 Evaluate side-chains 86 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN B 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.199293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.177779 restraints weight = 7995.842| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 3.13 r_work: 0.3919 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6331 Z= 0.110 Angle : 0.505 7.812 8631 Z= 0.261 Chirality : 0.038 0.125 966 Planarity : 0.004 0.077 1048 Dihedral : 4.715 50.471 849 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.46 % Allowed : 16.92 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.18 (0.32), residues: 758 helix: 1.12 (0.27), residues: 375 sheet: -1.10 (0.49), residues: 106 loop : -1.40 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 241 TYR 0.019 0.001 TYR A 110 PHE 0.032 0.001 PHE A 311 TRP 0.007 0.001 TRP A 103 HIS 0.008 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6326) covalent geometry : angle 0.50443 / 0.26 ( 8619) SS BOND : bond 0.00084 / 0.04 ( 3) SS BOND : angle 0.35645 / 0.19 ( 6) hydrogen bonds : bond 0.03282 / 2.12 ( 306) hydrogen bonds : angle 4.13755 / 3.10 ( 897) link_NAG-ASN : bond 0.00203 / 0.12 ( 2) link_NAG-ASN : angle 0.82546 / 0.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8684 (ttp) cc_final: 0.8453 (ttp) REVERT: A 204 TRP cc_start: 0.6975 (p90) cc_final: 0.6293 (p90) REVERT: A 271 TRP cc_start: 0.5965 (p-90) cc_final: 0.5515 (p-90) REVERT: A 316 ASN cc_start: 0.7647 (t0) cc_final: 0.6952 (t0) REVERT: A 507 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7160 (tt) REVERT: A 606 GLU cc_start: 0.6145 (tt0) cc_final: 0.5824 (tt0) REVERT: A 615 GLU cc_start: 0.5409 (mp0) cc_final: 0.5006 (mm-30) REVERT: C 31 MET cc_start: 0.1938 (mtm) cc_final: 0.1673 (mpp) REVERT: C 62 GLN cc_start: 0.7297 (mm-40) cc_final: 0.6742 (mt0) REVERT: C 81 ARG cc_start: 0.7167 (tpm170) cc_final: 0.5351 (ptt90) REVERT: C 123 LYS cc_start: 0.7245 (mptt) cc_final: 0.6590 (tttm) REVERT: B 46 TYR cc_start: 0.5942 (m-80) cc_final: 0.5657 (m-80) outliers start: 16 outliers final: 12 residues processed: 82 average time/residue: 0.0686 time to fit residues: 7.6852 Evaluate side-chains 83 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN A 205 ASN C 26 GLN B 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.200111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.178761 restraints weight = 8048.525| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.05 r_work: 0.3920 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6331 Z= 0.116 Angle : 0.513 7.807 8631 Z= 0.265 Chirality : 0.038 0.130 966 Planarity : 0.004 0.077 1048 Dihedral : 4.730 50.721 849 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.92 % Allowed : 17.23 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.12 (0.32), residues: 758 helix: 1.13 (0.27), residues: 375 sheet: -1.06 (0.49), residues: 106 loop : -1.32 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.022 0.001 TYR A 176 PHE 0.034 0.001 PHE A 311 TRP 0.006 0.001 TRP B 55 HIS 0.008 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 6326) covalent geometry : angle 0.51310 / 0.26 ( 8619) SS BOND : bond 0.00104 / 0.06 ( 3) SS BOND : angle 0.44463 / 0.24 ( 6) hydrogen bonds : bond 0.03318 / 2.15 ( 306) hydrogen bonds : angle 4.10621 / 3.08 ( 897) link_NAG-ASN : bond 0.00198 / 0.11 ( 2) link_NAG-ASN : angle 0.84700 / 0.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8663 (ttp) cc_final: 0.8432 (ttp) REVERT: A 204 TRP cc_start: 0.6721 (p90) cc_final: 0.6271 (p90) REVERT: A 271 TRP cc_start: 0.5899 (p-90) cc_final: 0.5392 (p-90) REVERT: A 316 ASN cc_start: 0.7378 (t0) cc_final: 0.6637 (t0) REVERT: A 507 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6839 (tt) REVERT: A 606 GLU cc_start: 0.6225 (tt0) cc_final: 0.5917 (tt0) REVERT: A 615 GLU cc_start: 0.5446 (mp0) cc_final: 0.4951 (mp0) REVERT: C 31 MET cc_start: 0.1809 (mtm) cc_final: 0.1529 (mpp) REVERT: C 62 GLN cc_start: 0.6966 (mm-40) cc_final: 0.6447 (mt0) REVERT: C 81 ARG cc_start: 0.7041 (tpm170) cc_final: 0.5160 (ptt90) REVERT: C 123 LYS cc_start: 0.7134 (mptt) cc_final: 0.6411 (tttm) REVERT: B 46 TYR cc_start: 0.6070 (m-80) cc_final: 0.5742 (m-80) outliers start: 19 outliers final: 13 residues processed: 85 average time/residue: 0.0687 time to fit residues: 8.0932 Evaluate side-chains 83 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 60 optimal weight: 0.0370 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.200543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.178648 restraints weight = 8012.687| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 3.14 r_work: 0.3913 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6331 Z= 0.112 Angle : 0.525 7.817 8631 Z= 0.272 Chirality : 0.039 0.127 966 Planarity : 0.004 0.076 1048 Dihedral : 4.792 50.773 849 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.62 % Allowed : 18.00 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.05 (0.32), residues: 758 helix: 1.13 (0.27), residues: 375 sheet: -0.92 (0.50), residues: 106 loop : -1.24 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.022 0.001 TYR A 176 PHE 0.033 0.001 PHE A 311 TRP 0.007 0.001 TRP B 66 HIS 0.008 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6326) covalent geometry : angle 0.52443 / 0.27 ( 8619) SS BOND : bond 0.00227 / 0.14 ( 3) SS BOND : angle 0.48209 / 0.22 ( 6) hydrogen bonds : bond 0.03292 / 2.13 ( 306) hydrogen bonds : angle 4.12608 / 3.10 ( 897) link_NAG-ASN : bond 0.00270 / 0.16 ( 2) link_NAG-ASN : angle 0.76567 / 0.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TRP cc_start: 0.7141 (p90) cc_final: 0.6448 (p90) REVERT: A 271 TRP cc_start: 0.6097 (p-90) cc_final: 0.5651 (p-90) REVERT: A 316 ASN cc_start: 0.7644 (t0) cc_final: 0.6936 (t0) REVERT: A 507 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7144 (tt) REVERT: A 615 GLU cc_start: 0.5514 (mp0) cc_final: 0.5001 (mp0) REVERT: C 48 ASP cc_start: 0.7468 (t0) cc_final: 0.7219 (t0) REVERT: C 62 GLN cc_start: 0.7302 (mm-40) cc_final: 0.6749 (mt0) REVERT: C 81 ARG cc_start: 0.7179 (tpm170) cc_final: 0.5379 (ptt90) REVERT: C 123 LYS cc_start: 0.7232 (mptt) cc_final: 0.6615 (tttm) REVERT: B 46 TYR cc_start: 0.5945 (m-80) cc_final: 0.5656 (m-80) outliers start: 17 outliers final: 14 residues processed: 83 average time/residue: 0.0660 time to fit residues: 7.5956 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.0770 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 0.0270 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.0000 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.203449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.181558 restraints weight = 7977.628| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 3.14 r_work: 0.3978 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6331 Z= 0.090 Angle : 0.501 7.615 8631 Z= 0.257 Chirality : 0.037 0.123 966 Planarity : 0.004 0.075 1048 Dihedral : 4.624 49.130 849 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.31 % Allowed : 18.62 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: 0.08 (0.32), residues: 758 helix: 1.27 (0.27), residues: 375 sheet: -0.87 (0.51), residues: 106 loop : -1.21 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.021 0.001 TYR A 176 PHE 0.034 0.001 PHE A 311 TRP 0.007 0.001 TRP B 55 HIS 0.005 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 ( 6326) covalent geometry : angle 0.50055 / 0.26 ( 8619) SS BOND : bond 0.00117 / 0.07 ( 3) SS BOND : angle 0.42910 / 0.20 ( 6) hydrogen bonds : bond 0.03028 / 1.95 ( 306) hydrogen bonds : angle 4.01394 / 3.03 ( 897) link_NAG-ASN : bond 0.00241 / 0.14 ( 2) link_NAG-ASN : angle 0.73462 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7383 (mmp) cc_final: 0.6817 (mmp) REVERT: A 271 TRP cc_start: 0.5767 (p-90) cc_final: 0.5515 (p-90) REVERT: A 316 ASN cc_start: 0.7203 (t0) cc_final: 0.6466 (t0) REVERT: A 440 PHE cc_start: 0.6209 (m-10) cc_final: 0.5717 (m-80) REVERT: A 507 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6717 (tt) REVERT: A 615 GLU cc_start: 0.5265 (mp0) cc_final: 0.4797 (mp0) REVERT: C 31 MET cc_start: 0.1702 (mtm) cc_final: 0.1466 (mpp) REVERT: C 48 ASP cc_start: 0.7433 (t0) cc_final: 0.7196 (t0) REVERT: C 62 GLN cc_start: 0.6725 (mm-40) cc_final: 0.6265 (mt0) REVERT: C 81 ARG cc_start: 0.6973 (tpm170) cc_final: 0.5129 (ptt90) REVERT: C 123 LYS cc_start: 0.7071 (mptt) cc_final: 0.6388 (tttm) REVERT: B 46 TYR cc_start: 0.6088 (m-80) cc_final: 0.5754 (m-80) outliers start: 15 outliers final: 12 residues processed: 87 average time/residue: 0.0707 time to fit residues: 8.5896 Evaluate side-chains 85 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.199251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.177449 restraints weight = 8097.543| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 3.16 r_work: 0.3929 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6331 Z= 0.116 Angle : 0.524 7.752 8631 Z= 0.271 Chirality : 0.040 0.276 966 Planarity : 0.004 0.077 1048 Dihedral : 4.761 50.736 849 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.85 % Allowed : 19.54 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: 0.03 (0.32), residues: 758 helix: 1.17 (0.27), residues: 380 sheet: -0.79 (0.51), residues: 106 loop : -1.23 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.021 0.001 TYR A 176 PHE 0.033 0.001 PHE A 311 TRP 0.006 0.001 TRP A 197 HIS 0.008 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6326) covalent geometry : angle 0.52392 / 0.27 ( 8619) SS BOND : bond 0.00104 / 0.06 ( 3) SS BOND : angle 0.43905 / 0.19 ( 6) hydrogen bonds : bond 0.03259 / 2.11 ( 306) hydrogen bonds : angle 4.02244 / 3.02 ( 897) link_NAG-ASN : bond 0.00240 / 0.14 ( 2) link_NAG-ASN : angle 0.72474 / 0.37 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 TRP cc_start: 0.6030 (p-90) cc_final: 0.5797 (p-90) REVERT: A 316 ASN cc_start: 0.7572 (t0) cc_final: 0.6856 (t0) REVERT: A 507 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7121 (tt) REVERT: A 615 GLU cc_start: 0.5477 (mp0) cc_final: 0.4927 (mp0) REVERT: C 48 ASP cc_start: 0.7506 (t0) cc_final: 0.7267 (t0) REVERT: C 62 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6687 (mt0) REVERT: C 81 ARG cc_start: 0.7087 (tpm170) cc_final: 0.5270 (ptt90) REVERT: C 123 LYS cc_start: 0.7245 (mptt) cc_final: 0.6642 (tttm) REVERT: B 46 TYR cc_start: 0.6026 (m-80) cc_final: 0.5721 (m-80) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 0.0688 time to fit residues: 7.6006 Evaluate side-chains 82 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 5 optimal weight: 0.0570 chunk 12 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN B 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.199757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.178479 restraints weight = 7966.408| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 3.03 r_work: 0.3951 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6331 Z= 0.110 Angle : 0.523 7.776 8631 Z= 0.270 Chirality : 0.039 0.269 966 Planarity : 0.004 0.076 1048 Dihedral : 4.778 50.335 849 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.00 % Allowed : 19.85 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: 0.24 (0.32), residues: 758 helix: 1.33 (0.27), residues: 373 sheet: -0.70 (0.51), residues: 106 loop : -1.05 (0.41), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.021 0.001 TYR A 176 PHE 0.033 0.001 PHE A 311 TRP 0.006 0.001 TRP A 197 HIS 0.007 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6326) covalent geometry : angle 0.52247 / 0.27 ( 8619) SS BOND : bond 0.00106 / 0.06 ( 3) SS BOND : angle 0.43609 / 0.21 ( 6) hydrogen bonds : bond 0.03252 / 2.10 ( 306) hydrogen bonds : angle 4.00792 / 3.01 ( 897) link_NAG-ASN : bond 0.00229 / 0.13 ( 2) link_NAG-ASN : angle 0.70788 / 0.36 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.37 seconds wall clock time: 24 minutes 53.38 seconds (1493.38 seconds total)