Starting phenix.real_space_refine on Thu Jul 2 04:36:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7li7_23362/07_2026/7li7_23362.cif Found real_map, /net/cci-nas-00/data/ceres_data/7li7_23362/07_2026/7li7_23362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7li7_23362/07_2026/7li7_23362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7li7_23362/07_2026/7li7_23362.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7li7_23362/07_2026/7li7_23362.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7li7_23362/07_2026/7li7_23362.cif" model { file = "/net/cci-nas-00/data/ceres_data/7li7_23362/07_2026/7li7_23362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7li7_23362/07_2026/7li7_23362.cif" } resolution = 4.1 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4101 2.51 5 N 960 2.21 5 O 1082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6177 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4292 Classifications: {'peptide': 537} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 514} Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 114 Unusual residues: {'CLR': 1, 'D10': 1, 'D12': 3, 'HP6': 5, 'LNK': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 1.42, per 1000 atoms: 0.23 Number of scatterers: 6177 At special positions: 0 Unit cell: (71.928, 73.224, 121.176, 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 34 16.00 O 1082 8.00 N 960 7.00 C 4101 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 B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 421.0 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 54.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 98 through 113 Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.758A pdb=" N LEU A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 Proline residue: A 131 - end of helix removed outlier: 3.841A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 removed outlier: 3.849A pdb=" N TRP A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 159 through 190 removed outlier: 4.289A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.615A pdb=" N HIS A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 271 Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.730A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 300 removed outlier: 4.143A pdb=" N TYR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 356 through 391 Processing helix chain 'A' and resid 403 through 417 removed outlier: 4.240A pdb=" N PHE A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 448 removed outlier: 3.836A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.608A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 removed outlier: 4.125A pdb=" N LYS A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 484 removed outlier: 3.708A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 483 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 496 Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 517 through 530 removed outlier: 4.456A pdb=" N ASP A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.768A pdb=" N ILE A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 603 through 612 Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.711A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.559A pdb=" N ARG B 69 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.559A pdb=" N ARG B 69 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.515A pdb=" N ALA C 39 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE C 95 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR C 94 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.241A pdb=" N LEU C 31 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 126 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR C 110 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 111 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.241A pdb=" N LEU C 31 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 126 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR C 110 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 121 " --> pdb=" O GLN C 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.587A pdb=" N ASN C 51 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 72 through 73 319 hydrogen bonds defined for protein. 900 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: 0.72 Time building geometry restraints manager: 0.85 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: 1814 1.34 - 1.46: 1597 1.46 - 1.58: 2889 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6349 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.64e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.40e-02 5.10e+03 1.35e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.21e+00 ... (remaining 6344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 8434 1.88 - 3.75: 125 3.75 - 5.63: 49 5.63 - 7.50: 3 7.50 - 9.38: 1 Bond angle restraints: 8612 Sorted by residual: angle pdb=" C GLU C 47 " pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 121.70 131.08 -9.38 1.80e+00 3.09e-01 2.71e+01 angle pdb=" N TRP A 197 " pdb=" CA TRP A 197 " pdb=" C TRP A 197 " ideal model delta sigma weight residual 114.56 111.00 3.56 1.27e+00 6.20e-01 7.84e+00 angle pdb=" C13 CLR A 710 " pdb=" C17 CLR A 710 " pdb=" C20 CLR A 710 " ideal model delta sigma weight residual 119.60 112.55 7.05 3.00e+00 1.11e-01 5.52e+00 angle pdb=" C20 CLR A 710 " pdb=" C22 CLR A 710 " pdb=" C23 CLR A 710 " ideal model delta sigma weight residual 115.57 108.76 6.81 3.00e+00 1.11e-01 5.16e+00 angle pdb=" CA GLU C 47 " pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 115.49 118.10 -2.61 1.24e+00 6.50e-01 4.42e+00 ... (remaining 8607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3293 17.81 - 35.61: 280 35.61 - 53.42: 32 53.42 - 71.23: 5 71.23 - 89.03: 2 Dihedral angle restraints: 3612 sinusoidal: 1412 harmonic: 2200 Sorted by residual: dihedral pdb=" CB GLU A 453 " pdb=" CG GLU A 453 " pdb=" CD GLU A 453 " pdb=" OE1 GLU A 453 " ideal model delta sinusoidal sigma weight residual 0.00 89.03 -89.03 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 136 " pdb=" CG GLU A 136 " pdb=" CD GLU A 136 " pdb=" OE1 GLU A 136 " ideal model delta sinusoidal sigma weight residual 0.00 -84.87 84.87 1 3.00e+01 1.11e-03 9.71e+00 dihedral pdb=" CA ARG A 596 " pdb=" CB ARG A 596 " pdb=" CG ARG A 596 " pdb=" CD ARG A 596 " ideal model delta sinusoidal sigma weight residual 180.00 122.06 57.94 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 945 0.234 - 0.469: 2 0.469 - 0.703: 0 0.703 - 0.937: 0 0.937 - 1.171: 1 Chirality restraints: 948 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-02 2.50e+03 3.43e+03 chirality pdb=" C14 CLR A 710 " pdb=" C13 CLR A 710 " pdb=" C15 CLR A 710 " pdb=" C8 CLR A 710 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C9 CLR A 710 " pdb=" C10 CLR A 710 " pdb=" C11 CLR A 710 " pdb=" C8 CLR A 710 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 945 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 402 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 403 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 403 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 403 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 100 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO C 101 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 101 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 101 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 589 " -0.016 5.00e-02 4.00e+02 2.41e-02 9.26e-01 pdb=" N PRO A 590 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 590 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 590 " -0.014 5.00e-02 4.00e+02 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1874 2.82 - 3.34: 5815 3.34 - 3.86: 10355 3.86 - 4.38: 11298 4.38 - 4.90: 19568 Nonbonded interactions: 48910 Sorted by model distance: nonbonded pdb=" OH TYR A 110 " pdb=" O VAL A 397 " model vdw 2.297 3.040 nonbonded pdb=" O ASN A 112 " pdb=" NZ LYS A 319 " model vdw 2.304 3.120 nonbonded pdb=" O THR A 600 " pdb=" NE ARG A 607 " model vdw 2.304 3.120 nonbonded pdb=" OD1 ASN A 101 " pdb=" NE2 GLN A 332 " model vdw 2.311 3.120 nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.313 3.040 ... (remaining 48905 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: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.150 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 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 : 0.002 0.065 6355 Z= 0.121 Angle : 0.644 11.827 8624 Z= 0.305 Chirality : 0.056 1.171 948 Planarity : 0.003 0.034 1047 Dihedral : 12.212 89.034 2207 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -2.70 (0.27), residues: 759 helix: -0.80 (0.24), residues: 370 sheet: -1.58 (0.54), residues: 81 loop : -3.08 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 152 TYR 0.012 0.001 TYR A 176 PHE 0.016 0.001 PHE A 474 TRP 0.006 0.001 TRP A 204 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 6349) covalent geometry : angle 0.61140 / 0.30 ( 8612) SS BOND : bond 0.00107 / 0.05 ( 3) SS BOND : angle 0.27710 / 0.16 ( 6) hydrogen bonds : bond 0.13463 / 8.83 ( 315) hydrogen bonds : angle 5.43678 / 3.84 ( 900) Misc. bond : bond 0.00023 / 0.01 ( 1) link_BETA1-4 : bond 0.06491 / 3.42 ( 1) link_BETA1-4 : angle 10.90698 / 5.95 ( 3) link_NAG-ASN : bond 0.00491 / 0.26 ( 1) link_NAG-ASN : angle 0.99914 / 0.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.4133 (mmmt) cc_final: 0.3539 (mmtp) REVERT: A 260 MET cc_start: 0.6095 (mmm) cc_final: 0.4405 (tmm) REVERT: A 267 TYR cc_start: 0.7045 (t80) cc_final: 0.6839 (t80) REVERT: A 456 HIS cc_start: 0.7952 (p-80) cc_final: 0.7737 (p90) REVERT: A 463 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6779 (mm-30) REVERT: A 478 LEU cc_start: 0.6966 (tt) cc_final: 0.6669 (tp) REVERT: A 514 TRP cc_start: 0.6695 (m100) cc_final: 0.6023 (m-10) REVERT: B 29 GLU cc_start: 0.8859 (mp0) cc_final: 0.8552 (mp0) REVERT: B 88 THR cc_start: 0.9257 (m) cc_final: 0.8963 (p) REVERT: B 125 PHE cc_start: 0.8290 (m-80) cc_final: 0.7889 (m-10) REVERT: C 33 VAL cc_start: 0.8265 (m) cc_final: 0.8057 (p) REVERT: C 66 GLN cc_start: 0.7811 (mp10) cc_final: 0.7283 (mp10) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0968 time to fit residues: 19.1189 Evaluate side-chains 117 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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: 0.4980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 58 GLN B 132 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.201207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.193110 restraints weight = 7675.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.193058 restraints weight = 11859.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.176380 restraints weight = 11779.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.174630 restraints weight = 11333.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.174315 restraints weight = 11603.345| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 6355 Z= 0.162 Angle : 0.585 9.439 8624 Z= 0.306 Chirality : 0.041 0.190 948 Planarity : 0.005 0.072 1047 Dihedral : 4.415 36.610 897 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.31 % Allowed : 5.92 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.93 (0.29), residues: 759 helix: -0.02 (0.26), residues: 371 sheet: -1.85 (0.52), residues: 91 loop : -2.72 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 307 TYR 0.014 0.002 TYR B 99 PHE 0.021 0.002 PHE A 474 TRP 0.027 0.001 TRP A 317 HIS 0.004 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 6349) covalent geometry : angle 0.58420 / 0.31 ( 8612) SS BOND : bond 0.00487 / 0.25 ( 3) SS BOND : angle 1.16815 / 0.69 ( 6) hydrogen bonds : bond 0.03396 / 2.14 ( 315) hydrogen bonds : angle 4.47024 / 3.21 ( 900) Misc. bond : bond 0.00071 / 0.04 ( 1) link_BETA1-4 : bond 0.01436 / 0.76 ( 1) link_BETA1-4 : angle 0.82407 / 0.43 ( 3) link_NAG-ASN : bond 0.00689 / 0.36 ( 1) link_NAG-ASN : angle 0.52697 / 0.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 201 LYS cc_start: 0.5181 (mmmt) cc_final: 0.4577 (mmmt) REVERT: A 291 ILE cc_start: 0.8593 (mm) cc_final: 0.8382 (mm) REVERT: A 456 HIS cc_start: 0.7209 (p-80) cc_final: 0.6995 (p90) REVERT: B 32 LYS cc_start: 0.6602 (mmpt) cc_final: 0.6318 (mmmt) REVERT: B 58 GLN cc_start: 0.8749 (tt0) cc_final: 0.8444 (tt0) REVERT: C 62 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: C 103 GLU cc_start: 0.7773 (mp0) cc_final: 0.7559 (mp0) REVERT: C 106 ASP cc_start: 0.8221 (m-30) cc_final: 0.8010 (m-30) outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.0756 time to fit residues: 14.4125 Evaluate side-chains 117 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 0.0570 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN C 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.201364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.193409 restraints weight = 7604.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.192189 restraints weight = 12668.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.178466 restraints weight = 13156.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.176217 restraints weight = 12694.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.176321 restraints weight = 11256.913| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6355 Z= 0.135 Angle : 0.551 9.497 8624 Z= 0.285 Chirality : 0.041 0.153 948 Planarity : 0.005 0.065 1047 Dihedral : 4.480 33.875 897 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.46 (0.30), residues: 759 helix: 0.24 (0.26), residues: 372 sheet: -1.41 (0.53), residues: 91 loop : -2.39 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 38 TYR 0.016 0.001 TYR B 99 PHE 0.018 0.001 PHE A 474 TRP 0.017 0.001 TRP A 541 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 6349) covalent geometry : angle 0.55058 / 0.28 ( 8612) SS BOND : bond 0.01090 / 0.55 ( 3) SS BOND : angle 0.65964 / 0.43 ( 6) hydrogen bonds : bond 0.03229 / 2.02 ( 315) hydrogen bonds : angle 4.37904 / 3.14 ( 900) Misc. bond : bond 0.00017 / 0.01 ( 1) link_BETA1-4 : bond 0.00308 / 0.16 ( 1) link_BETA1-4 : angle 0.42398 / 0.22 ( 3) link_NAG-ASN : bond 0.00486 / 0.26 ( 1) link_NAG-ASN : angle 0.66904 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 197 TRP cc_start: 0.7435 (m-90) cc_final: 0.7213 (m-90) REVERT: A 201 LYS cc_start: 0.5039 (mmmt) cc_final: 0.4553 (mmtt) REVERT: C 85 ARG cc_start: 0.7143 (mtm-85) cc_final: 0.6926 (mtm110) REVERT: C 106 ASP cc_start: 0.8191 (m-30) cc_final: 0.7823 (m-30) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.0768 time to fit residues: 14.5737 Evaluate side-chains 113 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.0270 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 141 GLN A 217 ASN A 223 HIS A 235 HIS B 58 GLN B 132 GLN C 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.190255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.180417 restraints weight = 7537.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.157939 restraints weight = 11715.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.157956 restraints weight = 12516.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.157956 restraints weight = 11707.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.157956 restraints weight = 11707.017| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 6355 Z= 0.190 Angle : 0.609 9.778 8624 Z= 0.324 Chirality : 0.042 0.155 948 Planarity : 0.005 0.066 1047 Dihedral : 5.034 32.289 897 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.62 % Allowed : 4.21 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.40 (0.30), residues: 759 helix: 0.34 (0.27), residues: 369 sheet: -1.34 (0.51), residues: 100 loop : -2.45 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 38 TYR 0.017 0.002 TYR A 186 PHE 0.021 0.002 PHE A 474 TRP 0.020 0.001 TRP A 541 HIS 0.005 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 ( 6349) covalent geometry : angle 0.60795 / 0.32 ( 8612) SS BOND : bond 0.00576 / 0.29 ( 3) SS BOND : angle 1.30266 / 0.75 ( 6) hydrogen bonds : bond 0.03622 / 2.28 ( 315) hydrogen bonds : angle 4.53863 / 3.22 ( 900) Misc. bond : bond 0.00030 / 0.02 ( 1) link_BETA1-4 : bond 0.00219 / 0.12 ( 1) link_BETA1-4 : angle 0.60616 / 0.33 ( 3) link_NAG-ASN : bond 0.00584 / 0.31 ( 1) link_NAG-ASN : angle 0.66241 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.228 Fit side-chains REVERT: A 201 LYS cc_start: 0.5427 (mmmt) cc_final: 0.4866 (mmtt) REVERT: A 456 HIS cc_start: 0.7208 (p90) cc_final: 0.6954 (p90) REVERT: B 65 GLU cc_start: 0.7598 (mt-10) cc_final: 0.6858 (mt-10) REVERT: C 33 VAL cc_start: 0.8646 (m) cc_final: 0.8409 (p) outliers start: 4 outliers final: 1 residues processed: 133 average time/residue: 0.0673 time to fit residues: 12.3252 Evaluate side-chains 113 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 141 GLN A 223 HIS A 569 ASN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN C 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.190317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.180541 restraints weight = 7695.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.162807 restraints weight = 11768.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.161794 restraints weight = 14436.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.161452 restraints weight = 13298.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.161938 restraints weight = 10585.792| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6355 Z= 0.172 Angle : 0.622 9.855 8624 Z= 0.323 Chirality : 0.043 0.218 948 Planarity : 0.005 0.072 1047 Dihedral : 5.176 31.085 897 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.31 % Allowed : 2.96 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.30), residues: 759 helix: 0.36 (0.27), residues: 364 sheet: -1.18 (0.51), residues: 100 loop : -2.24 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 38 TYR 0.017 0.002 TYR A 107 PHE 0.022 0.002 PHE A 474 TRP 0.024 0.001 TRP A 541 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 6349) covalent geometry : angle 0.62152 / 0.32 ( 8612) SS BOND : bond 0.00107 / 0.05 ( 3) SS BOND : angle 1.19765 / 0.68 ( 6) hydrogen bonds : bond 0.03516 / 2.20 ( 315) hydrogen bonds : angle 4.53697 / 3.23 ( 900) Misc. bond : bond 0.00055 / 0.03 ( 1) link_BETA1-4 : bond 0.00234 / 0.12 ( 1) link_BETA1-4 : angle 0.90475 / 0.49 ( 3) link_NAG-ASN : bond 0.00648 / 0.34 ( 1) link_NAG-ASN : angle 1.13706 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.227 Fit side-chains REVERT: A 141 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7322 (pp30) REVERT: A 201 LYS cc_start: 0.5620 (mmmt) cc_final: 0.4794 (mmmt) REVERT: A 456 HIS cc_start: 0.7057 (p90) cc_final: 0.6777 (p90) REVERT: B 109 ASP cc_start: 0.8364 (p0) cc_final: 0.8075 (p0) REVERT: C 33 VAL cc_start: 0.8590 (m) cc_final: 0.8387 (p) REVERT: C 62 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8153 (tt0) outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 0.0715 time to fit residues: 13.1695 Evaluate side-chains 112 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 0.0870 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 223 HIS C 62 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.192836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.183944 restraints weight = 7570.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.162706 restraints weight = 12058.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.162797 restraints weight = 11557.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.163016 restraints weight = 11702.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.162997 restraints weight = 10341.197| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6355 Z= 0.149 Angle : 0.600 9.862 8624 Z= 0.313 Chirality : 0.042 0.206 948 Planarity : 0.005 0.070 1047 Dihedral : 5.146 30.484 897 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.17 (0.30), residues: 759 helix: 0.39 (0.27), residues: 366 sheet: -1.01 (0.53), residues: 95 loop : -2.18 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 85 TYR 0.018 0.002 TYR A 107 PHE 0.018 0.001 PHE A 474 TRP 0.028 0.001 TRP A 317 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 6349) covalent geometry : angle 0.59852 / 0.31 ( 8612) SS BOND : bond 0.00304 / 0.16 ( 3) SS BOND : angle 1.35309 / 0.75 ( 6) hydrogen bonds : bond 0.03484 / 2.17 ( 315) hydrogen bonds : angle 4.46482 / 3.18 ( 900) Misc. bond : bond 0.00009 / 0.00 ( 1) link_BETA1-4 : bond 0.00342 / 0.18 ( 1) link_BETA1-4 : angle 0.68765 / 0.38 ( 3) link_NAG-ASN : bond 0.00635 / 0.33 ( 1) link_NAG-ASN : angle 1.11624 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.263 Fit side-chains REVERT: A 201 LYS cc_start: 0.5511 (mmmt) cc_final: 0.4692 (mmmt) REVERT: A 456 HIS cc_start: 0.7105 (p90) cc_final: 0.6782 (p90) REVERT: B 109 ASP cc_start: 0.8429 (p0) cc_final: 0.8181 (p0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0780 time to fit residues: 13.4749 Evaluate side-chains 114 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 223 HIS C 62 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.191846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.184833 restraints weight = 7532.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.184768 restraints weight = 11852.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.161631 restraints weight = 12001.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.161659 restraints weight = 13034.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.161844 restraints weight = 11339.703| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6355 Z= 0.147 Angle : 0.599 9.771 8624 Z= 0.312 Chirality : 0.041 0.185 948 Planarity : 0.005 0.070 1047 Dihedral : 5.144 30.287 897 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.16 % Allowed : 1.71 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.02 (0.30), residues: 759 helix: 0.52 (0.27), residues: 366 sheet: -0.93 (0.52), residues: 100 loop : -2.12 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 607 TYR 0.017 0.001 TYR A 107 PHE 0.020 0.001 PHE A 556 TRP 0.037 0.001 TRP A 317 HIS 0.004 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 6349) covalent geometry : angle 0.59767 / 0.31 ( 8612) SS BOND : bond 0.00164 / 0.09 ( 3) SS BOND : angle 1.41928 / 0.80 ( 6) hydrogen bonds : bond 0.03437 / 2.17 ( 315) hydrogen bonds : angle 4.43360 / 3.15 ( 900) Misc. bond : bond 0.00014 / 0.01 ( 1) link_BETA1-4 : bond 0.00300 / 0.16 ( 1) link_BETA1-4 : angle 0.62785 / 0.34 ( 3) link_NAG-ASN : bond 0.00605 / 0.32 ( 1) link_NAG-ASN : angle 0.82152 / 0.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.220 Fit side-chains REVERT: A 201 LYS cc_start: 0.5541 (mmmt) cc_final: 0.4688 (mmmt) REVERT: A 267 TYR cc_start: 0.8161 (t80) cc_final: 0.7925 (t80) REVERT: A 291 ILE cc_start: 0.8762 (mm) cc_final: 0.8560 (mm) REVERT: A 390 ARG cc_start: 0.7041 (tpt-90) cc_final: 0.5967 (ttm170) REVERT: A 456 HIS cc_start: 0.7192 (p90) cc_final: 0.6838 (p90) REVERT: B 64 LEU cc_start: 0.8049 (mt) cc_final: 0.7822 (mt) REVERT: B 109 ASP cc_start: 0.8442 (p0) cc_final: 0.8146 (p0) REVERT: C 62 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8097 (tt0) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.0730 time to fit residues: 13.5386 Evaluate side-chains 119 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.0270 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 223 HIS C 62 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.192402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.183410 restraints weight = 7543.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.163098 restraints weight = 11840.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.161972 restraints weight = 10948.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.161451 restraints weight = 11285.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.161777 restraints weight = 11117.362| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6355 Z= 0.146 Angle : 0.624 9.730 8624 Z= 0.324 Chirality : 0.042 0.182 948 Planarity : 0.005 0.071 1047 Dihedral : 5.172 30.619 897 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.97 (0.31), residues: 759 helix: 0.54 (0.27), residues: 364 sheet: -0.81 (0.54), residues: 98 loop : -2.07 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 59 TYR 0.019 0.002 TYR B 99 PHE 0.022 0.002 PHE A 556 TRP 0.046 0.001 TRP A 317 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 6349) covalent geometry : angle 0.62272 / 0.32 ( 8612) SS BOND : bond 0.00358 / 0.18 ( 3) SS BOND : angle 1.55494 / 0.86 ( 6) hydrogen bonds : bond 0.03484 / 2.20 ( 315) hydrogen bonds : angle 4.43443 / 3.14 ( 900) Misc. bond : bond 0.00010 / 0.01 ( 1) link_BETA1-4 : bond 0.00255 / 0.13 ( 1) link_BETA1-4 : angle 0.56331 / 0.31 ( 3) link_NAG-ASN : bond 0.00656 / 0.35 ( 1) link_NAG-ASN : angle 0.84439 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.211 Fit side-chains REVERT: A 201 LYS cc_start: 0.5478 (mmmt) cc_final: 0.4689 (mmmt) REVERT: A 390 ARG cc_start: 0.7049 (tpt-90) cc_final: 0.5562 (ttm170) REVERT: A 456 HIS cc_start: 0.7122 (p90) cc_final: 0.6756 (p90) REVERT: B 59 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7550 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0707 time to fit residues: 13.4816 Evaluate side-chains 115 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.0170 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 57 optimal weight: 0.0020 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.3826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 223 HIS C 62 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.193991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.185646 restraints weight = 7493.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.164637 restraints weight = 11378.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.163896 restraints weight = 12047.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.164300 restraints weight = 10337.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.164550 restraints weight = 9909.035| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6355 Z= 0.130 Angle : 0.611 9.693 8624 Z= 0.315 Chirality : 0.042 0.179 948 Planarity : 0.005 0.073 1047 Dihedral : 5.029 30.794 897 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.16 % Allowed : 0.31 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.82 (0.31), residues: 759 helix: 0.68 (0.27), residues: 363 sheet: -0.67 (0.54), residues: 103 loop : -2.07 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 38 TYR 0.046 0.002 TYR B 99 PHE 0.022 0.001 PHE A 474 TRP 0.045 0.001 TRP A 317 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 6349) covalent geometry : angle 0.60930 / 0.31 ( 8612) SS BOND : bond 0.00302 / 0.15 ( 3) SS BOND : angle 1.52367 / 0.83 ( 6) hydrogen bonds : bond 0.03357 / 2.13 ( 315) hydrogen bonds : angle 4.39951 / 3.12 ( 900) Misc. bond : bond 0.00004 / 0.00 ( 1) link_BETA1-4 : bond 0.00396 / 0.21 ( 1) link_BETA1-4 : angle 0.69573 / 0.38 ( 3) link_NAG-ASN : bond 0.00628 / 0.33 ( 1) link_NAG-ASN : angle 0.95800 / 0.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.180 Fit side-chains REVERT: A 201 LYS cc_start: 0.5404 (mmmt) cc_final: 0.4613 (mmmt) REVERT: A 390 ARG cc_start: 0.6958 (tpt-90) cc_final: 0.5586 (ttm170) REVERT: A 456 HIS cc_start: 0.7144 (p90) cc_final: 0.6771 (p90) REVERT: B 32 LYS cc_start: 0.6049 (mmmt) cc_final: 0.5671 (mmmt) REVERT: B 59 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7640 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 130 average time/residue: 0.0669 time to fit residues: 11.9633 Evaluate side-chains 110 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 0.1980 chunk 46 optimal weight: 0.3980 chunk 13 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 23 optimal weight: 0.0020 chunk 18 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 223 HIS C 62 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.194994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.187479 restraints weight = 7574.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.186206 restraints weight = 12194.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.173347 restraints weight = 12416.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.169842 restraints weight = 11407.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.170140 restraints weight = 11052.707| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6355 Z= 0.129 Angle : 0.619 11.551 8624 Z= 0.321 Chirality : 0.042 0.178 948 Planarity : 0.005 0.074 1047 Dihedral : 5.104 30.910 897 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.86 (0.31), residues: 759 helix: 0.64 (0.27), residues: 363 sheet: -0.68 (0.54), residues: 103 loop : -2.07 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 59 TYR 0.022 0.001 TYR B 99 PHE 0.023 0.001 PHE A 127 TRP 0.052 0.001 TRP A 317 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 6349) covalent geometry : angle 0.61797 / 0.32 ( 8612) SS BOND : bond 0.00126 / 0.06 ( 3) SS BOND : angle 1.56388 / 0.85 ( 6) hydrogen bonds : bond 0.03308 / 2.10 ( 315) hydrogen bonds : angle 4.39422 / 3.12 ( 900) Misc. bond : bond 0.00001 / 0.00 ( 1) link_BETA1-4 : bond 0.00312 / 0.16 ( 1) link_BETA1-4 : angle 0.64234 / 0.35 ( 3) link_NAG-ASN : bond 0.00662 / 0.35 ( 1) link_NAG-ASN : angle 0.97890 / 0.53 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.217 Fit side-chains REVERT: A 201 LYS cc_start: 0.5360 (mmmt) cc_final: 0.4585 (mmmt) REVERT: A 390 ARG cc_start: 0.6969 (tpt-90) cc_final: 0.5619 (ttm170) REVERT: A 456 HIS cc_start: 0.6955 (p90) cc_final: 0.6577 (p90) REVERT: A 536 PHE cc_start: 0.7813 (t80) cc_final: 0.7433 (t80) REVERT: B 32 LYS cc_start: 0.6386 (mmmt) cc_final: 0.6002 (mmmt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0720 time to fit residues: 12.1797 Evaluate side-chains 110 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 32 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 0.0170 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 223 HIS C 62 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.191139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.183225 restraints weight = 7465.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.182138 restraints weight = 12873.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.180406 restraints weight = 14126.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.179740 restraints weight = 13355.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.179027 restraints weight = 11891.802| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6355 Z= 0.148 Angle : 0.625 11.277 8624 Z= 0.325 Chirality : 0.042 0.177 948 Planarity : 0.005 0.074 1047 Dihedral : 5.105 31.225 897 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.16 % Allowed : 0.47 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.84 (0.31), residues: 759 helix: 0.66 (0.27), residues: 364 sheet: -0.76 (0.53), residues: 103 loop : -2.04 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 607 TYR 0.044 0.002 TYR A 410 PHE 0.021 0.001 PHE A 556 TRP 0.023 0.001 TRP A 317 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 6349) covalent geometry : angle 0.62403 / 0.32 ( 8612) SS BOND : bond 0.00110 / 0.06 ( 3) SS BOND : angle 1.58325 / 0.87 ( 6) hydrogen bonds : bond 0.03376 / 2.13 ( 315) hydrogen bonds : angle 4.37315 / 3.10 ( 900) Misc. bond : bond 0.00015 / 0.01 ( 1) link_BETA1-4 : bond 0.00328 / 0.17 ( 1) link_BETA1-4 : angle 0.71217 / 0.38 ( 3) link_NAG-ASN : bond 0.00646 / 0.34 ( 1) link_NAG-ASN : angle 0.81750 / 0.45 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1188.88 seconds wall clock time: 21 minutes 17.48 seconds (1277.48 seconds total)