Starting phenix.real_space_refine on Thu Jul 24 21:47:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7li7_23362/07_2025/7li7_23362.cif Found real_map, /net/cci-nas-00/data/ceres_data/7li7_23362/07_2025/7li7_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_2025/7li7_23362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7li7_23362/07_2025/7li7_23362.map" model { file = "/net/cci-nas-00/data/ceres_data/7li7_23362/07_2025/7li7_23362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7li7_23362/07_2025/7li7_23362.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 6 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: 6.91, per 1000 atoms: 1.12 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: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.84 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: 2.46 Time building geometry restraints manager: 2.27 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: 3379 17.81 - 35.61: 284 35.61 - 53.42: 40 53.42 - 71.23: 5 71.23 - 89.03: 2 Dihedral angle restraints: 3710 sinusoidal: 1510 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 3707 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: 7.260 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 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 : 12.289 89.034 2305 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (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 TRP 0.006 0.001 TRP A 204 HIS 0.001 0.000 HIS A 143 PHE 0.016 0.001 PHE A 474 TYR 0.012 0.001 TYR A 176 ARG 0.006 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 1) link_NAG-ASN : angle 0.99914 ( 3) link_BETA1-4 : bond 0.06491 ( 1) link_BETA1-4 : angle 10.90698 ( 3) hydrogen bonds : bond 0.13463 ( 315) hydrogen bonds : angle 5.43678 ( 900) SS BOND : bond 0.00107 ( 3) SS BOND : angle 0.27710 ( 6) covalent geometry : bond 0.00223 ( 6349) covalent geometry : angle 0.61140 ( 8612) Misc. bond : bond 0.00023 ( 1) *********************** 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 : 1.251 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: 0.6096 (mmm) cc_final: 0.4406 (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: 0.7888 (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: 0.2953 time to fit residues: 59.0588 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 : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.0040 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 68 optimal weight: 5.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4201 r_free = 0.4201 target = 0.211047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.204440 restraints weight = 7560.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.189007 restraints weight = 11338.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.188367 restraints weight = 12310.987| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6355 Z= 0.124 Angle : 0.536 9.396 8624 Z= 0.278 Chirality : 0.040 0.178 948 Planarity : 0.005 0.076 1047 Dihedral : 5.766 59.557 995 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.31 % Allowed : 4.36 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.29), residues: 759 helix: -0.04 (0.26), residues: 370 sheet: -1.62 (0.53), residues: 90 loop : -2.73 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 317 HIS 0.002 0.001 HIS A 143 PHE 0.015 0.001 PHE A 474 TYR 0.016 0.002 TYR B 99 ARG 0.004 0.000 ARG A 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 1) link_NAG-ASN : angle 0.67375 ( 3) link_BETA1-4 : bond 0.01229 ( 1) link_BETA1-4 : angle 0.37681 ( 3) hydrogen bonds : bond 0.03097 ( 315) hydrogen bonds : angle 4.44374 ( 900) SS BOND : bond 0.00234 ( 3) SS BOND : angle 0.94421 ( 6) covalent geometry : bond 0.00294 ( 6349) covalent geometry : angle 0.53537 ( 8612) Misc. bond : bond 0.00024 ( 1) *********************** 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 144 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.4728 (mmmt) cc_final: 0.4487 (mmmt) REVERT: B 32 LYS cc_start: 0.6416 (mmpt) cc_final: 0.6174 (mmmt) REVERT: B 57 LYS cc_start: 0.8983 (tttm) cc_final: 0.8665 (ttmm) REVERT: B 109 ASP cc_start: 0.8531 (p0) cc_final: 0.8090 (p0) REVERT: C 103 GLU cc_start: 0.7469 (mp0) cc_final: 0.7249 (mp0) REVERT: C 106 ASP cc_start: 0.8067 (m-30) cc_final: 0.7788 (m-30) outliers start: 2 outliers final: 0 residues processed: 143 average time/residue: 0.1893 time to fit residues: 35.5884 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 : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 49 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 332 GLN ** 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 = 0.4156 r_free = 0.4156 target = 0.206409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.197044 restraints weight = 7636.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.179554 restraints weight = 10989.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.180258 restraints weight = 10319.218| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6355 Z= 0.124 Angle : 0.538 9.447 8624 Z= 0.278 Chirality : 0.040 0.153 948 Planarity : 0.004 0.062 1047 Dihedral : 5.743 59.831 995 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.31 % Allowed : 5.30 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.30), residues: 759 helix: 0.26 (0.26), residues: 374 sheet: -1.56 (0.51), residues: 100 loop : -2.54 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 541 HIS 0.003 0.001 HIS A 143 PHE 0.019 0.001 PHE A 474 TYR 0.013 0.001 TYR B 99 ARG 0.005 0.000 ARG A 596 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 1) link_NAG-ASN : angle 0.61834 ( 3) link_BETA1-4 : bond 0.00450 ( 1) link_BETA1-4 : angle 0.69094 ( 3) hydrogen bonds : bond 0.03115 ( 315) hydrogen bonds : angle 4.29552 ( 900) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.80190 ( 6) covalent geometry : bond 0.00294 ( 6349) covalent geometry : angle 0.53751 ( 8612) Misc. bond : bond 0.00022 ( 1) *********************** 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 139 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.4815 (mmmt) cc_final: 0.4327 (mmtp) REVERT: A 456 HIS cc_start: 0.7196 (p90) cc_final: 0.6961 (p90) REVERT: B 32 LYS cc_start: 0.6432 (mmpt) cc_final: 0.6171 (mmmt) REVERT: B 53 MET cc_start: 0.7951 (mmm) cc_final: 0.7738 (mmt) REVERT: C 62 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8359 (tt0) outliers start: 2 outliers final: 0 residues processed: 138 average time/residue: 0.1821 time to fit residues: 33.6103 Evaluate side-chains 116 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 0.5980 chunk 68 optimal weight: 0.1980 chunk 48 optimal weight: 0.3980 chunk 69 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 132 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.206928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.198918 restraints weight = 7651.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.181116 restraints weight = 11899.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.181669 restraints weight = 11955.377| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6355 Z= 0.113 Angle : 0.529 9.404 8624 Z= 0.272 Chirality : 0.040 0.157 948 Planarity : 0.004 0.056 1047 Dihedral : 5.751 59.419 995 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.16 % Allowed : 2.18 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.30), residues: 759 helix: 0.40 (0.26), residues: 378 sheet: -1.10 (0.54), residues: 98 loop : -2.41 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 317 HIS 0.002 0.001 HIS A 143 PHE 0.021 0.001 PHE A 474 TYR 0.013 0.001 TYR A 142 ARG 0.004 0.000 ARG C 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 1) link_NAG-ASN : angle 0.74829 ( 3) link_BETA1-4 : bond 0.00305 ( 1) link_BETA1-4 : angle 0.63960 ( 3) hydrogen bonds : bond 0.02957 ( 315) hydrogen bonds : angle 4.22812 ( 900) SS BOND : bond 0.00267 ( 3) SS BOND : angle 1.04244 ( 6) covalent geometry : bond 0.00266 ( 6349) covalent geometry : angle 0.52822 ( 8612) Misc. bond : bond 0.00017 ( 1) *********************** 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 138 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.724 Fit side-chains REVERT: A 201 LYS cc_start: 0.4840 (mmmt) cc_final: 0.4337 (mmtt) REVERT: A 456 HIS cc_start: 0.7115 (p90) cc_final: 0.6861 (p90) REVERT: B 53 MET cc_start: 0.8030 (mmm) cc_final: 0.7820 (mmt) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1923 time to fit residues: 34.7742 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 : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN B 58 GLN B 132 GLN C 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.198010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.173524 restraints weight = 7419.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.172109 restraints weight = 12608.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.171646 restraints weight = 12062.700| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6355 Z= 0.145 Angle : 0.570 9.511 8624 Z= 0.299 Chirality : 0.041 0.152 948 Planarity : 0.004 0.052 1047 Dihedral : 5.989 59.937 995 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.31 % Allowed : 2.49 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.30), residues: 759 helix: 0.52 (0.27), residues: 375 sheet: -1.06 (0.53), residues: 100 loop : -2.38 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 541 HIS 0.003 0.001 HIS A 143 PHE 0.024 0.002 PHE A 474 TYR 0.015 0.002 TYR B 99 ARG 0.009 0.001 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 1) link_NAG-ASN : angle 0.54276 ( 3) link_BETA1-4 : bond 0.00360 ( 1) link_BETA1-4 : angle 0.69774 ( 3) hydrogen bonds : bond 0.03257 ( 315) hydrogen bonds : angle 4.27960 ( 900) SS BOND : bond 0.00927 ( 3) SS BOND : angle 1.42536 ( 6) covalent geometry : bond 0.00347 ( 6349) covalent geometry : angle 0.56913 ( 8612) Misc. bond : bond 0.00025 ( 1) *********************** 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 137 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.681 Fit side-chains REVERT: A 201 LYS cc_start: 0.5282 (mmmt) cc_final: 0.4766 (mmtt) REVERT: A 456 HIS cc_start: 0.6956 (p90) cc_final: 0.6642 (p90) outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 0.1672 time to fit residues: 30.7287 Evaluate side-chains 109 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 29 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN A 217 ASN B 132 GLN C 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.195738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.186732 restraints weight = 7347.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.165038 restraints weight = 12190.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.165165 restraints weight = 10406.573| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6355 Z= 0.150 Angle : 0.582 9.701 8624 Z= 0.303 Chirality : 0.041 0.170 948 Planarity : 0.004 0.054 1047 Dihedral : 6.131 59.838 995 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.31 % Allowed : 2.02 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.30), residues: 759 helix: 0.43 (0.27), residues: 366 sheet: -0.87 (0.54), residues: 100 loop : -2.29 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 541 HIS 0.003 0.001 HIS A 143 PHE 0.022 0.002 PHE A 474 TYR 0.014 0.001 TYR A 186 ARG 0.003 0.000 ARG A 607 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 1) link_NAG-ASN : angle 0.66974 ( 3) link_BETA1-4 : bond 0.00456 ( 1) link_BETA1-4 : angle 0.74501 ( 3) hydrogen bonds : bond 0.03312 ( 315) hydrogen bonds : angle 4.37692 ( 900) SS BOND : bond 0.00133 ( 3) SS BOND : angle 1.40515 ( 6) covalent geometry : bond 0.00362 ( 6349) covalent geometry : angle 0.58139 ( 8612) Misc. bond : bond 0.00013 ( 1) *********************** 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 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.731 Fit side-chains REVERT: A 201 LYS cc_start: 0.5422 (mmmt) cc_final: 0.4912 (mmtt) REVERT: A 456 HIS cc_start: 0.7302 (p90) cc_final: 0.6950 (p90) REVERT: B 99 TYR cc_start: 0.8718 (m-10) cc_final: 0.8435 (m-10) REVERT: C 33 VAL cc_start: 0.8611 (m) cc_final: 0.8403 (p) REVERT: C 62 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8434 (tt0) outliers start: 2 outliers final: 0 residues processed: 131 average time/residue: 0.1699 time to fit residues: 30.2380 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 : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 7 optimal weight: 0.0170 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN A 235 HIS A 569 ASN C 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.195546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3849 r_free = 0.3849 target = 0.174835 restraints weight = 7571.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.173724 restraints weight = 8961.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.173656 restraints weight = 11160.043| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6355 Z= 0.147 Angle : 0.594 9.659 8624 Z= 0.306 Chirality : 0.042 0.193 948 Planarity : 0.004 0.050 1047 Dihedral : 6.196 59.671 995 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.16 % Allowed : 1.09 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.30), residues: 759 helix: 0.53 (0.27), residues: 363 sheet: -0.75 (0.54), residues: 100 loop : -2.23 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 541 HIS 0.003 0.001 HIS A 143 PHE 0.017 0.001 PHE A 474 TYR 0.017 0.001 TYR A 186 ARG 0.010 0.001 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 1) link_NAG-ASN : angle 0.73972 ( 3) link_BETA1-4 : bond 0.00281 ( 1) link_BETA1-4 : angle 0.74701 ( 3) hydrogen bonds : bond 0.03342 ( 315) hydrogen bonds : angle 4.39708 ( 900) SS BOND : bond 0.00089 ( 3) SS BOND : angle 1.58164 ( 6) covalent geometry : bond 0.00354 ( 6349) covalent geometry : angle 0.59251 ( 8612) Misc. bond : bond 0.00018 ( 1) *********************** 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 135 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.698 Fit side-chains REVERT: A 201 LYS cc_start: 0.5508 (mmmt) cc_final: 0.4722 (mmmt) REVERT: A 291 ILE cc_start: 0.8804 (mm) cc_final: 0.8538 (mm) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1553 time to fit residues: 28.9294 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 : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 61 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.197618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.188698 restraints weight = 7347.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.188277 restraints weight = 12203.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.170197 restraints weight = 11513.631| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6355 Z= 0.123 Angle : 0.571 9.517 8624 Z= 0.297 Chirality : 0.041 0.237 948 Planarity : 0.004 0.075 1047 Dihedral : 6.165 59.775 995 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.16 % Allowed : 1.25 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.31), residues: 759 helix: 0.49 (0.27), residues: 365 sheet: -0.64 (0.57), residues: 95 loop : -2.13 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 541 HIS 0.002 0.001 HIS A 143 PHE 0.021 0.001 PHE A 127 TYR 0.026 0.001 TYR B 99 ARG 0.006 0.001 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00693 ( 1) link_NAG-ASN : angle 1.31826 ( 3) link_BETA1-4 : bond 0.00225 ( 1) link_BETA1-4 : angle 0.86699 ( 3) hydrogen bonds : bond 0.03175 ( 315) hydrogen bonds : angle 4.30185 ( 900) SS BOND : bond 0.00264 ( 3) SS BOND : angle 0.84551 ( 6) covalent geometry : bond 0.00290 ( 6349) covalent geometry : angle 0.56989 ( 8612) Misc. bond : bond 0.00004 ( 1) *********************** 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 124 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.705 Fit side-chains REVERT: A 141 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7237 (pp30) REVERT: A 197 TRP cc_start: 0.8022 (m-90) cc_final: 0.7155 (m-90) REVERT: A 201 LYS cc_start: 0.5434 (mmmt) cc_final: 0.4610 (mmmt) REVERT: A 456 HIS cc_start: 0.6983 (p90) cc_final: 0.6708 (p90) REVERT: C 112 CYS cc_start: 0.6098 (p) cc_final: 0.5809 (p) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1718 time to fit residues: 28.5539 Evaluate side-chains 109 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.192995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.167352 restraints weight = 7528.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.165547 restraints weight = 12224.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.165647 restraints weight = 14246.315| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6355 Z= 0.155 Angle : 0.601 9.496 8624 Z= 0.315 Chirality : 0.043 0.195 948 Planarity : 0.005 0.074 1047 Dihedral : 6.274 59.498 995 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.30), residues: 759 helix: 0.47 (0.27), residues: 365 sheet: -0.70 (0.55), residues: 100 loop : -2.25 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 541 HIS 0.004 0.001 HIS A 143 PHE 0.021 0.002 PHE A 474 TYR 0.036 0.002 TYR A 410 ARG 0.007 0.000 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 1) link_NAG-ASN : angle 0.80038 ( 3) link_BETA1-4 : bond 0.00131 ( 1) link_BETA1-4 : angle 0.66274 ( 3) hydrogen bonds : bond 0.03412 ( 315) hydrogen bonds : angle 4.39705 ( 900) SS BOND : bond 0.00152 ( 3) SS BOND : angle 1.29345 ( 6) covalent geometry : bond 0.00371 ( 6349) covalent geometry : angle 0.60020 ( 8612) Misc. bond : bond 0.00031 ( 1) *********************** 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 127 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.670 Fit side-chains REVERT: A 201 LYS cc_start: 0.5585 (mmmt) cc_final: 0.4774 (mmmt) REVERT: A 291 ILE cc_start: 0.8775 (mm) cc_final: 0.8525 (mm) REVERT: A 456 HIS cc_start: 0.6918 (p90) cc_final: 0.6590 (p90) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1608 time to fit residues: 28.0075 Evaluate side-chains 111 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 28 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.188419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.177929 restraints weight = 7520.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.175162 restraints weight = 15608.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.173357 restraints weight = 16017.525| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4247 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 : 0.653 9.800 8624 Z= 0.344 Chirality : 0.044 0.179 948 Planarity : 0.005 0.075 1047 Dihedral : 6.591 59.010 995 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.30), residues: 759 helix: 0.31 (0.27), residues: 372 sheet: -0.74 (0.55), residues: 100 loop : -2.18 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 317 HIS 0.005 0.001 HIS A 143 PHE 0.025 0.002 PHE A 556 TYR 0.029 0.002 TYR A 410 ARG 0.004 0.000 ARG A 390 Details of bonding type rmsd link_NAG-ASN : bond 0.00680 ( 1) link_NAG-ASN : angle 0.65281 ( 3) link_BETA1-4 : bond 0.00203 ( 1) link_BETA1-4 : angle 0.80417 ( 3) hydrogen bonds : bond 0.03790 ( 315) hydrogen bonds : angle 4.58103 ( 900) SS BOND : bond 0.00221 ( 3) SS BOND : angle 1.53831 ( 6) covalent geometry : bond 0.00463 ( 6349) covalent geometry : angle 0.65219 ( 8612) Misc. bond : bond 0.00023 ( 1) ********************** 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 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.660 Fit side-chains REVERT: A 186 TYR cc_start: 0.8614 (m-10) cc_final: 0.8206 (m-10) REVERT: A 201 LYS cc_start: 0.5856 (mmmt) cc_final: 0.4936 (mmmt) REVERT: A 291 ILE cc_start: 0.8950 (mm) cc_final: 0.8644 (mm) REVERT: A 414 ILE cc_start: 0.7698 (mm) cc_final: 0.7268 (mm) REVERT: A 456 HIS cc_start: 0.6473 (p90) cc_final: 0.6176 (p90) REVERT: B 86 LYS cc_start: 0.6544 (ptmt) cc_final: 0.6264 (tttt) REVERT: B 99 TYR cc_start: 0.9052 (m-80) cc_final: 0.8755 (m-10) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1556 time to fit residues: 26.9995 Evaluate side-chains 112 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.0070 chunk 6 optimal weight: 0.0020 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 74 optimal weight: 0.0670 overall best weight: 0.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.197232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.188823 restraints weight = 7542.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.167875 restraints weight = 11358.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.168403 restraints weight = 10948.548| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6355 Z= 0.120 Angle : 0.597 9.739 8624 Z= 0.309 Chirality : 0.042 0.214 948 Planarity : 0.005 0.076 1047 Dihedral : 6.403 59.577 995 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.30), residues: 759 helix: 0.36 (0.26), residues: 371 sheet: -0.47 (0.56), residues: 96 loop : -2.03 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 317 HIS 0.002 0.001 HIS A 143 PHE 0.018 0.001 PHE A 474 TYR 0.035 0.002 TYR A 410 ARG 0.003 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00633 ( 1) link_NAG-ASN : angle 1.45209 ( 3) link_BETA1-4 : bond 0.00379 ( 1) link_BETA1-4 : angle 0.78827 ( 3) hydrogen bonds : bond 0.03208 ( 315) hydrogen bonds : angle 4.40148 ( 900) SS BOND : bond 0.00189 ( 3) SS BOND : angle 1.44154 ( 6) covalent geometry : bond 0.00279 ( 6349) covalent geometry : angle 0.59557 ( 8612) Misc. bond : bond 0.00007 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.79 seconds wall clock time: 46 minutes 30.31 seconds (2790.31 seconds total)