Starting phenix.real_space_refine on Tue Aug 4 15:21:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yt7_73444/08_2026/9yt7_73444.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yt7_73444/08_2026/9yt7_73444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yt7_73444/08_2026/9yt7_73444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yt7_73444/08_2026/9yt7_73444.map" model { file = "/net/cci-nas-00/data/ceres_data/9yt7_73444/08_2026/9yt7_73444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yt7_73444/08_2026/9yt7_73444.cif" } resolution = 2.76 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= 0.000 sd= 0.013 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 18 5.16 5 C 2713 2.51 5 N 675 2.21 5 O 799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4205 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1957 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain breaks: 4 Chain: "C" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2122 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 17, 'TRANS': 249} Chain breaks: 1 Chain: "A" 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: "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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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 Time building chain proxies: 1.11, per 1000 atoms: 0.26 Number of scatterers: 4205 At special positions: 0 Unit cell: (78.208, 89.024, 91.52, 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 18 16.00 O 799 8.00 N 675 7.00 C 2713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 163 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 1 " - " ASN B 278 " " NAG B1301 " - " ASN B 230 " " NAG B1302 " - " ASN B 120 " " NAG B1303 " - " ASN B 241 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG D 1 " - " ASN C 354 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 154.1 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 7.6% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.634A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.890A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 29 removed outlier: 7.848A pdb=" N ASN B 61 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR B 265 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP B 260 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 187 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE B 198 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP B 224 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE B 200 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.738A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.840A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.699A pdb=" N GLY B 101 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 239 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE B 99 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 118 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 169 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 165 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLU B 130 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N CYS B 163 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLN B 132 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N ASN B 161 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.579A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) 135 hydrogen bonds defined for protein. 321 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: 0.74 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1280 1.34 - 1.46: 946 1.46 - 1.58: 2069 1.58 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 4316 Sorted by residual: bond pdb=" N ILE B 68 " pdb=" CA ILE B 68 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.09e-02 8.42e+03 1.26e+01 bond pdb=" N VAL B 128 " pdb=" CA VAL B 128 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.19e-02 7.06e+03 9.07e+00 bond pdb=" N LYS B 95 " pdb=" CA LYS B 95 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.16e-02 7.43e+03 8.66e+00 bond pdb=" N GLU C 583 " pdb=" CA GLU C 583 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.31e+00 bond pdb=" N ILE B 194 " pdb=" CA ILE B 194 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.14e-02 7.69e+03 7.31e+00 ... (remaining 4311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 5511 1.36 - 2.72: 293 2.72 - 4.07: 55 4.07 - 5.43: 4 5.43 - 6.79: 3 Bond angle restraints: 5866 Sorted by residual: angle pdb=" CA LYS B 111 " pdb=" CB LYS B 111 " pdb=" CG LYS B 111 " ideal model delta sigma weight residual 114.10 120.89 -6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA LEU B 238 " pdb=" C LEU B 238 " pdb=" O LEU B 238 " ideal model delta sigma weight residual 121.89 118.03 3.86 1.17e+00 7.31e-01 1.09e+01 angle pdb=" CA ILE B 194 " pdb=" C ILE B 194 " pdb=" O ILE B 194 " ideal model delta sigma weight residual 121.28 117.90 3.38 1.06e+00 8.90e-01 1.01e+01 angle pdb=" CA PHE B 234 " pdb=" CB PHE B 234 " pdb=" CG PHE B 234 " ideal model delta sigma weight residual 113.80 116.95 -3.15 1.00e+00 1.00e+00 9.92e+00 angle pdb=" CA ASP B 195 " pdb=" C ASP B 195 " pdb=" O ASP B 195 " ideal model delta sigma weight residual 121.54 117.89 3.65 1.16e+00 7.43e-01 9.92e+00 ... (remaining 5861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 2379 16.59 - 33.18: 215 33.18 - 49.77: 38 49.77 - 66.37: 22 66.37 - 82.96: 3 Dihedral angle restraints: 2657 sinusoidal: 1166 harmonic: 1491 Sorted by residual: dihedral pdb=" SG CYS B 129 " pdb=" CB CYS B 163 " pdb=" SG CYS B 163 " pdb=" CA CYS B 163 " ideal model delta sinusoidal sigma weight residual 79.00 4.89 74.11 1 2.00e+01 2.50e-03 1.74e+01 dihedral pdb=" CA ASP C 428 " pdb=" CB ASP C 428 " pdb=" CG ASP C 428 " pdb=" OD1 ASP C 428 " ideal model delta sinusoidal sigma weight residual -30.00 -89.16 59.16 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 120.45 -27.45 1 1.00e+01 1.00e-02 1.08e+01 ... (remaining 2654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 461 0.044 - 0.088: 112 0.088 - 0.131: 68 0.131 - 0.175: 20 0.175 - 0.219: 9 Chirality restraints: 670 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.53e+00 chirality pdb=" CA ILE B 194 " pdb=" N ILE B 194 " pdb=" C ILE B 194 " pdb=" CB ILE B 194 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE B 22 " pdb=" N ILE B 22 " pdb=" C ILE B 22 " pdb=" CB ILE B 22 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 667 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 94 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C GLU B 94 " 0.023 2.00e-02 2.50e+03 pdb=" O GLU B 94 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS B 95 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO C 561 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 28 " 0.004 2.00e-02 2.50e+03 7.06e-03 9.96e-01 pdb=" CG TYR B 28 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR B 28 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 28 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 28 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 28 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 28 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 28 " -0.001 2.00e-02 2.50e+03 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 771 2.77 - 3.30: 3808 3.30 - 3.84: 6650 3.84 - 4.37: 8373 4.37 - 4.90: 14403 Nonbonded interactions: 34005 Sorted by model distance: nonbonded pdb=" OG SER B 110 " pdb=" OE1 GLN B 132 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.289 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.332 3.040 nonbonded pdb=" OD2 ASP B 140 " pdb=" NH2 ARG B 242 " model vdw 2.374 3.120 nonbonded pdb=" OG1 THR B 122 " pdb=" OD1 ASN B 123 " model vdw 2.429 3.040 ... (remaining 34000 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.520 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.220 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4331 Z= 0.294 Angle : 0.701 6.788 5905 Z= 0.441 Chirality : 0.056 0.219 670 Planarity : 0.003 0.032 740 Dihedral : 13.435 82.956 1679 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.22 % Allowed : 14.47 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.34), residues: 496 helix: -2.30 (0.87), residues: 26 sheet: -0.54 (0.39), residues: 148 loop : -0.82 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 242 TYR 0.017 0.001 TYR B 28 PHE 0.010 0.001 PHE B 43 TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.29 ( 4316) covalent geometry : angle 0.68951 / 0.44 ( 5866) SS BOND : bond 0.00982 / 0.52 ( 6) SS BOND : angle 1.10352 / 0.64 ( 12) hydrogen bonds : bond 0.21934 / 14.24 ( 133) hydrogen bonds : angle 10.15494 / 6.85 ( 321) link_BETA1-4 : bond 0.00159 / 0.08 ( 2) link_BETA1-4 : angle 2.55809 / 1.34 ( 6) link_NAG-ASN : bond 0.00214 / 0.16 ( 7) link_NAG-ASN : angle 1.66288 / 1.21 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.186 Fit side-chains REVERT: B 18 LEU cc_start: 0.9093 (mp) cc_final: 0.8738 (tt) REVERT: B 113 GLN cc_start: 0.8805 (mt0) cc_final: 0.8080 (mm110) REVERT: B 123 ASN cc_start: 0.8575 (m110) cc_final: 0.8206 (m-40) REVERT: B 132 GLN cc_start: 0.8997 (tp40) cc_final: 0.8071 (tp40) REVERT: B 153 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 194 ILE cc_start: 0.9330 (pt) cc_final: 0.8887 (pp) REVERT: C 378 LYS cc_start: 0.8719 (mttt) cc_final: 0.8208 (mtpm) REVERT: C 409 GLN cc_start: 0.8968 (mt0) cc_final: 0.8749 (mt0) REVERT: C 448 ASN cc_start: 0.7835 (t0) cc_final: 0.7197 (t0) REVERT: C 498 ARG cc_start: 0.8712 (ptp-170) cc_final: 0.8082 (ptp-110) REVERT: C 564 GLN cc_start: 0.9085 (mm110) cc_final: 0.8662 (mm110) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.8244 time to fit residues: 49.9010 Evaluate side-chains 47 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** 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 = 0.3496 r_free = 0.3496 target = 0.094703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.064485 restraints weight = 8266.813| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.52 r_work: 0.2758 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4331 Z= 0.140 Angle : 0.587 5.650 5905 Z= 0.307 Chirality : 0.047 0.160 670 Planarity : 0.004 0.029 740 Dihedral : 6.564 53.067 738 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.54 % Allowed : 17.32 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.35), residues: 496 helix: -2.34 (0.80), residues: 27 sheet: -0.30 (0.40), residues: 157 loop : -0.79 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 76 TYR 0.015 0.001 TYR B 261 PHE 0.019 0.001 PHE B 125 TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 4316) covalent geometry : angle 0.57495 / 0.30 ( 5866) SS BOND : bond 0.00060 / 0.03 ( 6) SS BOND : angle 0.45400 / 0.25 ( 12) hydrogen bonds : bond 0.04516 / 2.82 ( 133) hydrogen bonds : angle 7.50141 / 5.03 ( 321) link_BETA1-4 : bond 0.00327 / 0.16 ( 2) link_BETA1-4 : angle 2.69971 / 1.38 ( 6) link_NAG-ASN : bond 0.00208 / 0.11 ( 7) link_NAG-ASN : angle 1.54603 / 1.09 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.171 Fit side-chains REVERT: B 18 LEU cc_start: 0.9120 (mp) cc_final: 0.8735 (tt) REVERT: B 41 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.8945 (mtpt) REVERT: B 123 ASN cc_start: 0.8652 (m110) cc_final: 0.8350 (m-40) REVERT: B 132 GLN cc_start: 0.9028 (tp40) cc_final: 0.8221 (tp40) REVERT: B 153 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 277 GLU cc_start: 0.8684 (pm20) cc_final: 0.8424 (pm20) REVERT: C 378 LYS cc_start: 0.8737 (mttt) cc_final: 0.8204 (mtpm) REVERT: C 406 GLU cc_start: 0.8656 (mp0) cc_final: 0.8416 (mp0) REVERT: C 448 ASN cc_start: 0.7895 (t0) cc_final: 0.7106 (t0) REVERT: C 498 ARG cc_start: 0.8719 (ptp-170) cc_final: 0.8106 (ptp-110) REVERT: C 516 GLU cc_start: 0.8111 (tp30) cc_final: 0.7879 (tp30) REVERT: C 564 GLN cc_start: 0.9139 (mm110) cc_final: 0.8824 (mm-40) outliers start: 7 outliers final: 2 residues processed: 53 average time/residue: 0.8342 time to fit residues: 45.4362 Evaluate side-chains 46 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 586 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.0010 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 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 = 0.3493 r_free = 0.3493 target = 0.094646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.064246 restraints weight = 8192.585| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.53 r_work: 0.2745 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4331 Z= 0.159 Angle : 0.572 5.665 5905 Z= 0.298 Chirality : 0.047 0.160 670 Planarity : 0.004 0.028 740 Dihedral : 6.563 53.337 738 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.41 % Allowed : 16.67 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.35), residues: 496 helix: -2.40 (0.77), residues: 27 sheet: -0.00 (0.42), residues: 145 loop : -0.91 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.014 0.001 TYR B 261 PHE 0.019 0.001 PHE B 125 TRP 0.007 0.001 TRP C 353 HIS 0.003 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 4316) covalent geometry : angle 0.56060 / 0.30 ( 5866) SS BOND : bond 0.00120 / 0.06 ( 6) SS BOND : angle 0.39489 / 0.21 ( 12) hydrogen bonds : bond 0.03964 / 2.50 ( 133) hydrogen bonds : angle 7.06831 / 4.74 ( 321) link_BETA1-4 : bond 0.00244 / 0.12 ( 2) link_BETA1-4 : angle 2.60123 / 1.34 ( 6) link_NAG-ASN : bond 0.00214 / 0.12 ( 7) link_NAG-ASN : angle 1.47668 / 1.04 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.100 Fit side-chains REVERT: B 18 LEU cc_start: 0.9102 (mp) cc_final: 0.8711 (tt) REVERT: B 41 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.8990 (mtpt) REVERT: B 59 PHE cc_start: 0.8259 (m-80) cc_final: 0.7846 (m-80) REVERT: B 113 GLN cc_start: 0.8796 (mt0) cc_final: 0.8055 (mm110) REVERT: B 123 ASN cc_start: 0.8660 (m110) cc_final: 0.8381 (m-40) REVERT: B 132 GLN cc_start: 0.9069 (tp40) cc_final: 0.8245 (tp40) REVERT: B 153 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7852 (tm-30) REVERT: C 378 LYS cc_start: 0.8702 (mttt) cc_final: 0.8110 (mtpp) REVERT: C 406 GLU cc_start: 0.8526 (mp0) cc_final: 0.7987 (mp0) REVERT: C 448 ASN cc_start: 0.7939 (t0) cc_final: 0.7263 (t0) REVERT: C 498 ARG cc_start: 0.8729 (ptp-170) cc_final: 0.8132 (ptp-110) REVERT: C 516 GLU cc_start: 0.8153 (tp30) cc_final: 0.7941 (tp30) REVERT: C 564 GLN cc_start: 0.9180 (mm110) cc_final: 0.8803 (mm110) outliers start: 11 outliers final: 2 residues processed: 52 average time/residue: 0.6163 time to fit residues: 32.8997 Evaluate side-chains 46 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 586 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 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 = 0.3468 r_free = 0.3468 target = 0.093490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.062711 restraints weight = 8108.754| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.53 r_work: 0.2713 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 4331 Z= 0.225 Angle : 0.624 9.615 5905 Z= 0.324 Chirality : 0.048 0.163 670 Planarity : 0.004 0.028 740 Dihedral : 6.823 53.415 738 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.85 % Allowed : 17.76 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.35), residues: 496 helix: -2.41 (0.79), residues: 27 sheet: -0.03 (0.42), residues: 144 loop : -1.01 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 233 TYR 0.014 0.001 TYR B 261 PHE 0.019 0.001 PHE B 125 TRP 0.009 0.001 TRP C 353 HIS 0.003 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 ( 4316) covalent geometry : angle 0.59991 / 0.32 ( 5866) SS BOND : bond 0.00405 / 0.21 ( 6) SS BOND : angle 2.86734 / 1.68 ( 12) hydrogen bonds : bond 0.03874 / 2.46 ( 133) hydrogen bonds : angle 6.90903 / 4.63 ( 321) link_BETA1-4 : bond 0.00250 / 0.13 ( 2) link_BETA1-4 : angle 2.61506 / 1.35 ( 6) link_NAG-ASN : bond 0.00204 / 0.13 ( 7) link_NAG-ASN : angle 1.48137 / 1.05 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.161 Fit side-chains REVERT: B 18 LEU cc_start: 0.9106 (mp) cc_final: 0.8722 (tt) REVERT: B 41 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.8988 (mtpt) REVERT: B 59 PHE cc_start: 0.8236 (m-80) cc_final: 0.7801 (m-80) REVERT: B 123 ASN cc_start: 0.8640 (m110) cc_final: 0.8345 (m-40) REVERT: B 132 GLN cc_start: 0.9029 (tp40) cc_final: 0.8082 (tp40) REVERT: B 277 GLU cc_start: 0.8731 (pm20) cc_final: 0.8490 (pm20) REVERT: C 378 LYS cc_start: 0.8655 (mttt) cc_final: 0.8053 (mtpp) REVERT: C 406 GLU cc_start: 0.8519 (mp0) cc_final: 0.8021 (mp0) REVERT: C 448 ASN cc_start: 0.8038 (t0) cc_final: 0.7433 (t0) REVERT: C 498 ARG cc_start: 0.8733 (ptp-170) cc_final: 0.8154 (ptp-110) REVERT: C 564 GLN cc_start: 0.9182 (mm110) cc_final: 0.8756 (mm110) outliers start: 13 outliers final: 0 residues processed: 52 average time/residue: 0.8078 time to fit residues: 43.1866 Evaluate side-chains 41 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.0000 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 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 = 0.3488 r_free = 0.3488 target = 0.094055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.063719 restraints weight = 8223.892| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.60 r_work: 0.2791 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4331 Z= 0.174 Angle : 0.587 6.476 5905 Z= 0.305 Chirality : 0.047 0.160 670 Planarity : 0.003 0.027 740 Dihedral : 6.676 53.347 738 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.63 % Allowed : 18.20 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.35), residues: 496 helix: -2.45 (0.77), residues: 27 sheet: -0.13 (0.41), residues: 145 loop : -0.87 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 457 TYR 0.014 0.001 TYR B 261 PHE 0.018 0.001 PHE B 125 TRP 0.007 0.001 TRP C 353 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 4316) covalent geometry : angle 0.57103 / 0.30 ( 5866) SS BOND : bond 0.00125 / 0.06 ( 6) SS BOND : angle 1.84090 / 1.08 ( 12) hydrogen bonds : bond 0.03557 / 2.28 ( 133) hydrogen bonds : angle 6.71818 / 4.49 ( 321) link_BETA1-4 : bond 0.00238 / 0.12 ( 2) link_BETA1-4 : angle 2.52448 / 1.31 ( 6) link_NAG-ASN : bond 0.00197 / 0.12 ( 7) link_NAG-ASN : angle 1.42710 / 1.02 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.100 Fit side-chains REVERT: B 18 LEU cc_start: 0.9092 (mp) cc_final: 0.8711 (tt) REVERT: B 59 PHE cc_start: 0.8283 (m-80) cc_final: 0.7844 (m-80) REVERT: B 113 GLN cc_start: 0.8945 (mt0) cc_final: 0.8153 (mm110) REVERT: B 123 ASN cc_start: 0.8596 (m110) cc_final: 0.8333 (m-40) REVERT: B 132 GLN cc_start: 0.9067 (tp40) cc_final: 0.8412 (tp40) REVERT: B 277 GLU cc_start: 0.8758 (pm20) cc_final: 0.8507 (pm20) REVERT: C 378 LYS cc_start: 0.8634 (mttt) cc_final: 0.8027 (mtpp) REVERT: C 406 GLU cc_start: 0.8457 (mp0) cc_final: 0.7925 (mp0) REVERT: C 448 ASN cc_start: 0.8053 (t0) cc_final: 0.7371 (t0) REVERT: C 498 ARG cc_start: 0.8731 (ptp-170) cc_final: 0.8158 (ptp-110) REVERT: C 516 GLU cc_start: 0.8111 (tp30) cc_final: 0.7878 (tp30) REVERT: C 564 GLN cc_start: 0.9182 (mm110) cc_final: 0.8767 (mm110) outliers start: 12 outliers final: 4 residues processed: 54 average time/residue: 0.5998 time to fit residues: 33.2790 Evaluate side-chains 44 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 586 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 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 = 0.3483 r_free = 0.3483 target = 0.093831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.063428 restraints weight = 8396.814| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.62 r_work: 0.2785 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4331 Z= 0.180 Angle : 0.609 9.451 5905 Z= 0.315 Chirality : 0.047 0.160 670 Planarity : 0.003 0.027 740 Dihedral : 6.705 53.554 738 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.07 % Allowed : 18.20 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.35), residues: 496 helix: -2.40 (0.79), residues: 27 sheet: -0.11 (0.41), residues: 145 loop : -0.85 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 76 TYR 0.014 0.001 TYR B 261 PHE 0.022 0.001 PHE B 165 TRP 0.008 0.001 TRP C 353 HIS 0.002 0.000 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 4316) covalent geometry : angle 0.59169 / 0.31 ( 5866) SS BOND : bond 0.00251 / 0.13 ( 6) SS BOND : angle 2.08968 / 1.10 ( 12) hydrogen bonds : bond 0.03516 / 2.25 ( 133) hydrogen bonds : angle 6.71803 / 4.50 ( 321) link_BETA1-4 : bond 0.00239 / 0.12 ( 2) link_BETA1-4 : angle 2.50801 / 1.30 ( 6) link_NAG-ASN : bond 0.00193 / 0.12 ( 7) link_NAG-ASN : angle 1.43268 / 1.03 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.163 Fit side-chains REVERT: B 18 LEU cc_start: 0.9098 (mp) cc_final: 0.8700 (tt) REVERT: B 41 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9127 (mttt) REVERT: B 59 PHE cc_start: 0.8277 (m-80) cc_final: 0.7838 (m-80) REVERT: B 123 ASN cc_start: 0.8587 (m110) cc_final: 0.8317 (m-40) REVERT: B 132 GLN cc_start: 0.9029 (tp40) cc_final: 0.8426 (tp40) REVERT: B 153 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7902 (tm-30) REVERT: C 378 LYS cc_start: 0.8605 (mttt) cc_final: 0.7992 (mtpp) REVERT: C 403 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7439 (mtpt) REVERT: C 406 GLU cc_start: 0.8535 (mp0) cc_final: 0.7945 (mp0) REVERT: C 414 GLN cc_start: 0.9191 (tp40) cc_final: 0.8891 (tp40) REVERT: C 448 ASN cc_start: 0.8100 (t0) cc_final: 0.7459 (t0) REVERT: C 465 GLU cc_start: 0.8921 (tt0) cc_final: 0.8587 (tt0) REVERT: C 498 ARG cc_start: 0.8750 (ptp-170) cc_final: 0.8177 (ptp-110) REVERT: C 516 GLU cc_start: 0.8087 (tp30) cc_final: 0.7788 (tp30) REVERT: C 564 GLN cc_start: 0.9186 (mm110) cc_final: 0.8776 (mm110) outliers start: 14 outliers final: 3 residues processed: 51 average time/residue: 0.7488 time to fit residues: 39.3011 Evaluate side-chains 46 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 586 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 506 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 = 0.3460 r_free = 0.3460 target = 0.092423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.061835 restraints weight = 8474.478| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.62 r_work: 0.2752 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 4331 Z= 0.290 Angle : 0.682 9.408 5905 Z= 0.352 Chirality : 0.049 0.170 670 Planarity : 0.004 0.027 740 Dihedral : 7.110 54.206 738 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.41 % Allowed : 19.08 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.63 % 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: -1.12 (0.35), residues: 496 helix: -2.50 (0.79), residues: 27 sheet: -0.22 (0.39), residues: 154 loop : -0.84 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 233 TYR 0.015 0.002 TYR B 261 PHE 0.019 0.002 PHE B 165 TRP 0.011 0.002 TRP C 353 HIS 0.003 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.29 ( 4316) covalent geometry : angle 0.66380 / 0.35 ( 5866) SS BOND : bond 0.00246 / 0.12 ( 6) SS BOND : angle 2.36909 / 1.34 ( 12) hydrogen bonds : bond 0.03804 / 2.44 ( 133) hydrogen bonds : angle 6.82926 / 4.60 ( 321) link_BETA1-4 : bond 0.00114 / 0.06 ( 2) link_BETA1-4 : angle 2.58485 / 1.34 ( 6) link_NAG-ASN : bond 0.00222 / 0.17 ( 7) link_NAG-ASN : angle 1.60665 / 1.15 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.173 Fit side-chains REVERT: B 18 LEU cc_start: 0.9099 (mp) cc_final: 0.8702 (tt) REVERT: B 123 ASN cc_start: 0.8610 (m110) cc_final: 0.8306 (m-40) REVERT: B 132 GLN cc_start: 0.9010 (tp40) cc_final: 0.8326 (tp40) REVERT: B 277 GLU cc_start: 0.8755 (pm20) cc_final: 0.8514 (pm20) REVERT: C 378 LYS cc_start: 0.8602 (mttt) cc_final: 0.7980 (mtpp) REVERT: C 406 GLU cc_start: 0.8576 (mp0) cc_final: 0.8016 (mp0) REVERT: C 414 GLN cc_start: 0.9217 (tp40) cc_final: 0.8952 (tp40) REVERT: C 448 ASN cc_start: 0.8235 (t0) cc_final: 0.7699 (t0) REVERT: C 465 GLU cc_start: 0.8921 (tt0) cc_final: 0.8605 (tt0) REVERT: C 498 ARG cc_start: 0.8773 (ptp-170) cc_final: 0.8209 (ptp-110) REVERT: C 516 GLU cc_start: 0.8151 (tp30) cc_final: 0.7908 (tp30) outliers start: 11 outliers final: 4 residues processed: 50 average time/residue: 0.9147 time to fit residues: 46.9378 Evaluate side-chains 45 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 583 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** 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 = 0.3483 r_free = 0.3483 target = 0.093676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.063220 restraints weight = 8229.623| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.61 r_work: 0.2784 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4331 Z= 0.165 Angle : 0.618 7.901 5905 Z= 0.320 Chirality : 0.047 0.165 670 Planarity : 0.003 0.027 740 Dihedral : 6.943 53.832 738 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.41 % Allowed : 18.86 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -1.09 (0.35), residues: 496 helix: -2.45 (0.79), residues: 27 sheet: -0.14 (0.40), residues: 154 loop : -0.86 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 76 TYR 0.013 0.001 TYR B 261 PHE 0.023 0.001 PHE B 165 TRP 0.010 0.001 TRP C 353 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 4316) covalent geometry : angle 0.60036 / 0.32 ( 5866) SS BOND : bond 0.00102 / 0.06 ( 6) SS BOND : angle 2.11588 / 1.21 ( 12) hydrogen bonds : bond 0.03480 / 2.22 ( 133) hydrogen bonds : angle 6.74728 / 4.53 ( 321) link_BETA1-4 : bond 0.00195 / 0.10 ( 2) link_BETA1-4 : angle 2.50079 / 1.30 ( 6) link_NAG-ASN : bond 0.00133 / 0.09 ( 7) link_NAG-ASN : angle 1.50542 / 1.10 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.174 Fit side-chains REVERT: B 18 LEU cc_start: 0.9084 (mp) cc_final: 0.8692 (tt) REVERT: B 41 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9140 (mttt) REVERT: B 59 PHE cc_start: 0.8270 (m-80) cc_final: 0.7849 (m-80) REVERT: B 123 ASN cc_start: 0.8585 (m110) cc_final: 0.8304 (m-40) REVERT: B 132 GLN cc_start: 0.9051 (tp40) cc_final: 0.8352 (tp40) REVERT: B 153 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 378 LYS cc_start: 0.8605 (mttt) cc_final: 0.7983 (mtpp) REVERT: C 406 GLU cc_start: 0.8511 (mp0) cc_final: 0.7913 (mp0) REVERT: C 414 GLN cc_start: 0.9194 (tp40) cc_final: 0.8922 (tp40) REVERT: C 448 ASN cc_start: 0.8212 (t0) cc_final: 0.7540 (t0) REVERT: C 465 GLU cc_start: 0.8940 (tt0) cc_final: 0.8606 (tt0) REVERT: C 498 ARG cc_start: 0.8763 (ptp-170) cc_final: 0.8191 (ptp-110) REVERT: C 516 GLU cc_start: 0.8151 (tp30) cc_final: 0.7907 (tp30) REVERT: C 564 GLN cc_start: 0.9219 (mm110) cc_final: 0.8817 (mm110) outliers start: 11 outliers final: 2 residues processed: 52 average time/residue: 0.7645 time to fit residues: 40.8950 Evaluate side-chains 45 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 402 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 0.3980 chunk 19 optimal weight: 0.0010 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 506 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 = 0.3525 r_free = 0.3525 target = 0.096255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.065533 restraints weight = 8380.083| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.68 r_work: 0.2840 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4331 Z= 0.117 Angle : 0.595 7.469 5905 Z= 0.308 Chirality : 0.046 0.147 670 Planarity : 0.003 0.027 740 Dihedral : 6.699 52.911 738 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.10 % Allowed : 20.39 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.36), residues: 496 helix: -2.38 (0.81), residues: 27 sheet: 0.05 (0.40), residues: 155 loop : -0.72 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 76 TYR 0.015 0.001 TYR B 261 PHE 0.027 0.001 PHE B 165 TRP 0.005 0.001 TRP C 353 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4316) covalent geometry : angle 0.57996 / 0.30 ( 5866) SS BOND : bond 0.00062 / 0.03 ( 6) SS BOND : angle 1.79122 / 1.03 ( 12) hydrogen bonds : bond 0.03226 / 2.07 ( 133) hydrogen bonds : angle 6.42358 / 4.29 ( 321) link_BETA1-4 : bond 0.00418 / 0.21 ( 2) link_BETA1-4 : angle 2.36790 / 1.23 ( 6) link_NAG-ASN : bond 0.00208 / 0.12 ( 7) link_NAG-ASN : angle 1.48296 / 1.06 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.171 Fit side-chains REVERT: B 18 LEU cc_start: 0.9058 (mp) cc_final: 0.8660 (tt) REVERT: B 28 TYR cc_start: 0.7250 (t80) cc_final: 0.7002 (t80) REVERT: B 41 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9121 (mttt) REVERT: B 59 PHE cc_start: 0.8355 (m-80) cc_final: 0.7896 (m-80) REVERT: B 132 GLN cc_start: 0.9073 (tp40) cc_final: 0.8426 (tp40) REVERT: B 153 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 232 THR cc_start: 0.8937 (m) cc_final: 0.8605 (p) REVERT: C 378 LYS cc_start: 0.8565 (mttt) cc_final: 0.7967 (mtpp) REVERT: C 406 GLU cc_start: 0.8526 (mp0) cc_final: 0.7974 (mp0) REVERT: C 414 GLN cc_start: 0.9195 (tp40) cc_final: 0.8948 (tp40) REVERT: C 448 ASN cc_start: 0.8113 (t0) cc_final: 0.7164 (t0) REVERT: C 465 GLU cc_start: 0.8985 (tt0) cc_final: 0.8646 (tt0) REVERT: C 498 ARG cc_start: 0.8760 (ptp-170) cc_final: 0.8151 (ptp-110) REVERT: C 516 GLU cc_start: 0.8146 (tp30) cc_final: 0.7869 (tp30) REVERT: C 564 GLN cc_start: 0.9210 (mm110) cc_final: 0.8845 (mm110) REVERT: C 586 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8479 (m-30) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 0.7180 time to fit residues: 37.6485 Evaluate side-chains 49 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 586 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.064918 restraints weight = 7987.206| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.46 r_work: 0.2771 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4331 Z= 0.135 Angle : 0.621 10.243 5905 Z= 0.318 Chirality : 0.047 0.242 670 Planarity : 0.003 0.029 740 Dihedral : 6.698 53.318 738 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.88 % Allowed : 20.83 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.36), residues: 496 helix: -2.42 (0.79), residues: 27 sheet: 0.16 (0.41), residues: 155 loop : -0.71 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 76 TYR 0.013 0.001 TYR B 261 PHE 0.025 0.001 PHE B 165 TRP 0.006 0.001 TRP C 353 HIS 0.002 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 4316) covalent geometry : angle 0.60705 / 0.32 ( 5866) SS BOND : bond 0.00100 / 0.05 ( 6) SS BOND : angle 1.74561 / 1.00 ( 12) hydrogen bonds : bond 0.03172 / 2.01 ( 133) hydrogen bonds : angle 6.38895 / 4.27 ( 321) link_BETA1-4 : bond 0.00357 / 0.18 ( 2) link_BETA1-4 : angle 2.34439 / 1.22 ( 6) link_NAG-ASN : bond 0.00165 / 0.09 ( 7) link_NAG-ASN : angle 1.45539 / 1.03 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.177 Fit side-chains REVERT: B 18 LEU cc_start: 0.9081 (mp) cc_final: 0.8689 (tt) REVERT: B 41 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9168 (mttt) REVERT: B 59 PHE cc_start: 0.8261 (m-80) cc_final: 0.7842 (m-80) REVERT: B 132 GLN cc_start: 0.9073 (tp40) cc_final: 0.8472 (tp40) REVERT: B 153 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 232 THR cc_start: 0.9026 (m) cc_final: 0.8727 (p) REVERT: C 378 LYS cc_start: 0.8662 (mttt) cc_final: 0.8076 (mtpp) REVERT: C 406 GLU cc_start: 0.8548 (mp0) cc_final: 0.8016 (mp0) REVERT: C 414 GLN cc_start: 0.9193 (tp40) cc_final: 0.8935 (tp40) REVERT: C 448 ASN cc_start: 0.8133 (t0) cc_final: 0.7279 (t0) REVERT: C 465 GLU cc_start: 0.8958 (tt0) cc_final: 0.8643 (tt0) REVERT: C 493 GLU cc_start: 0.7831 (mp0) cc_final: 0.7488 (mp0) REVERT: C 498 ARG cc_start: 0.8765 (ptp-170) cc_final: 0.8165 (ptp-110) REVERT: C 516 GLU cc_start: 0.8156 (tp30) cc_final: 0.7914 (tp30) REVERT: C 564 GLN cc_start: 0.9244 (mm110) cc_final: 0.8915 (mm110) REVERT: C 586 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8592 (m-30) outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.8177 time to fit residues: 41.0961 Evaluate side-chains 50 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 586 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.0370 chunk 12 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.0020 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.4466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 506 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 = 0.3528 r_free = 0.3528 target = 0.096301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.066202 restraints weight = 8136.156| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.50 r_work: 0.2790 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4331 Z= 0.121 Angle : 0.604 9.408 5905 Z= 0.312 Chirality : 0.047 0.219 670 Planarity : 0.003 0.027 740 Dihedral : 6.629 53.694 738 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.10 % Allowed : 20.61 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.36), residues: 496 helix: -2.34 (0.82), residues: 27 sheet: 0.48 (0.41), residues: 158 loop : -0.74 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 76 TYR 0.012 0.001 TYR B 261 PHE 0.025 0.001 PHE B 165 TRP 0.006 0.001 TRP C 353 HIS 0.002 0.000 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 4316) covalent geometry : angle 0.59189 / 0.31 ( 5866) SS BOND : bond 0.00117 / 0.06 ( 6) SS BOND : angle 1.64213 / 0.94 ( 12) hydrogen bonds : bond 0.03108 / 1.98 ( 133) hydrogen bonds : angle 6.18616 / 4.14 ( 321) link_BETA1-4 : bond 0.00365 / 0.19 ( 2) link_BETA1-4 : angle 2.23294 / 1.17 ( 6) link_NAG-ASN : bond 0.00191 / 0.11 ( 7) link_NAG-ASN : angle 1.36878 / 0.98 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1711.94 seconds wall clock time: 29 minutes 56.20 seconds (1796.20 seconds total)