Starting phenix.real_space_refine on Wed Jul 1 22:13:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k9k_22751/07_2026/7k9k_22751.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k9k_22751/07_2026/7k9k_22751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7k9k_22751/07_2026/7k9k_22751.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k9k_22751/07_2026/7k9k_22751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k9k_22751/07_2026/7k9k_22751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k9k_22751/07_2026/7k9k_22751.map" model { file = "/net/cci-nas-00/data/ceres_data/7k9k_22751/07_2026/7k9k_22751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k9k_22751/07_2026/7k9k_22751.cif" } resolution = 3.14 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= 0.002 sd= 0.071 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 12 5.16 5 C 2035 2.51 5 N 524 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3202 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1400 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain breaks: 1 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.72, per 1000 atoms: 0.22 Number of scatterers: 3202 At special positions: 0 Unit cell: (79.2, 63.8, 77, 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 12 16.00 O 631 8.00 N 524 7.00 C 2035 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " BETA1-6 " NAG B 1 " - " FUC B 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 115.8 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 11.7% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.079A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.322A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.712A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.519A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'L' and resid 79 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.515A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.667A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 9 through 12 removed outlier: 7.133A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 9 through 12 removed outlier: 7.133A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.631A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER L 63 " --> pdb=" O SER L 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.817A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU L 104 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU L 53 " --> pdb=" O LYS L 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.817A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU L 104 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 107 hydrogen bonds defined for protein. 255 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: 0.34 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 517 1.32 - 1.45: 1013 1.45 - 1.57: 1740 1.57 - 1.70: 0 1.70 - 1.83: 14 Bond restraints: 3284 Sorted by residual: bond pdb=" C VAL A 433 " pdb=" O VAL A 433 " ideal model delta sigma weight residual 1.238 1.193 0.044 1.17e-02 7.31e+03 1.45e+01 bond pdb=" C CYS A 432 " pdb=" O CYS A 432 " ideal model delta sigma weight residual 1.235 1.198 0.038 1.14e-02 7.69e+03 1.09e+01 bond pdb=" N SER L 7 " pdb=" CA SER L 7 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.04e-02 9.25e+03 1.04e+01 bond pdb=" CA ALA A 435 " pdb=" CB ALA A 435 " ideal model delta sigma weight residual 1.535 1.482 0.053 1.90e-02 2.77e+03 7.83e+00 bond pdb=" CA SER L 7 " pdb=" CB SER L 7 " ideal model delta sigma weight residual 1.537 1.497 0.040 1.47e-02 4.63e+03 7.46e+00 ... (remaining 3279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 4002 1.40 - 2.79: 347 2.79 - 4.19: 85 4.19 - 5.58: 21 5.58 - 6.98: 10 Bond angle restraints: 4465 Sorted by residual: angle pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 117.96 122.41 -4.45 8.10e-01 1.52e+00 3.02e+01 angle pdb=" C PRO L 15 " pdb=" CA PRO L 15 " pdb=" CB PRO L 15 " ideal model delta sigma weight residual 111.46 105.66 5.80 1.29e+00 6.01e-01 2.02e+01 angle pdb=" N GLY L 16 " pdb=" CA GLY L 16 " pdb=" C GLY L 16 " ideal model delta sigma weight residual 113.79 108.80 4.99 1.17e+00 7.31e-01 1.82e+01 angle pdb=" CA ALA L 9 " pdb=" C ALA L 9 " pdb=" O ALA L 9 " ideal model delta sigma weight residual 120.55 116.59 3.96 1.06e+00 8.90e-01 1.39e+01 angle pdb=" CA VAL A 433 " pdb=" C VAL A 433 " pdb=" O VAL A 433 " ideal model delta sigma weight residual 120.57 116.93 3.64 1.07e+00 8.73e-01 1.16e+01 ... (remaining 4460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 1721 17.04 - 34.07: 133 34.07 - 51.11: 29 51.11 - 68.14: 6 68.14 - 85.17: 5 Dihedral angle restraints: 1894 sinusoidal: 729 harmonic: 1165 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -0.83 -85.17 1 1.00e+01 1.00e-02 8.79e+01 dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual 0.00 29.78 -29.78 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -41.61 -44.39 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 1891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 395 0.070 - 0.140: 83 0.140 - 0.210: 10 0.210 - 0.280: 2 0.280 - 0.350: 3 Chirality restraints: 493 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA PHE A 377 " pdb=" N PHE A 377 " pdb=" C PHE A 377 " pdb=" CB PHE A 377 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA GLN L 6 " pdb=" N GLN L 6 " pdb=" C GLN L 6 " pdb=" CB GLN L 6 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 490 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE L 58 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO L 59 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 431 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C GLY A 431 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY A 431 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS A 432 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 98 " -0.042 9.50e-02 1.11e+02 2.49e-02 3.50e+00 pdb=" NE ARG H 98 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG H 98 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG H 98 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG H 98 " 0.009 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 217 2.73 - 3.27: 3220 3.27 - 3.82: 4945 3.82 - 4.36: 6169 4.36 - 4.90: 10675 Nonbonded interactions: 25226 Sorted by model distance: nonbonded pdb=" OG SER H 17 " pdb=" O LEU H 83 " model vdw 2.188 3.040 nonbonded pdb=" O PHE H 107 " pdb=" NE1 TRP H 110 " model vdw 2.232 3.120 nonbonded pdb=" OG SER H 66 " pdb=" OE1 GLU H 67 " model vdw 2.243 3.040 nonbonded pdb=" N LEU A 455 " pdb=" O PRO A 491 " model vdw 2.270 3.120 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.301 3.040 ... (remaining 25221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.110 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 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 : 0.006 0.053 3293 Z= 0.340 Angle : 0.975 7.520 4487 Z= 0.558 Chirality : 0.063 0.350 493 Planarity : 0.005 0.055 565 Dihedral : 13.513 76.299 1139 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.35 (0.39), residues: 394 helix: -1.50 (0.85), residues: 34 sheet: -0.41 (0.41), residues: 129 loop : -1.06 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG H 98 TYR 0.028 0.003 TYR H 80 PHE 0.026 0.002 PHE A 497 TRP 0.025 0.003 TRP A 436 HIS 0.005 0.003 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.34 ( 3284) covalent geometry : angle 0.96045 / 0.56 ( 4465) SS BOND : bond 0.00741 / 0.36 ( 5) SS BOND : angle 1.77181 / 0.95 ( 10) hydrogen bonds : bond 0.26370 / 17.53 ( 100) hydrogen bonds : angle 10.78116 / 7.39 ( 255) link_BETA1-4 : bond 0.01425 / 0.74 ( 2) link_BETA1-4 : angle 3.58342 / 1.77 ( 6) link_BETA1-6 : bond 0.00546 / 0.29 ( 1) link_BETA1-6 : angle 2.29257 / 1.20 ( 3) link_NAG-ASN : bond 0.00496 / 0.26 ( 1) link_NAG-ASN : angle 2.97039 / 1.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.7791 (m-30) cc_final: 0.7456 (m-30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0543 time to fit residues: 5.3914 Evaluate side-chains 63 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 0.0270 chunk 37 optimal weight: 4.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 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 = 0.3858 r_free = 0.3858 target = 0.130665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109694 restraints weight = 5840.770| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.13 r_work: 0.3451 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3293 Z= 0.152 Angle : 0.727 10.429 4487 Z= 0.367 Chirality : 0.047 0.172 493 Planarity : 0.005 0.053 565 Dihedral : 5.389 18.171 443 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.73 % Allowed : 8.09 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.89 (0.41), residues: 394 helix: -1.49 (0.96), residues: 34 sheet: -0.10 (0.41), residues: 140 loop : -0.70 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 355 TYR 0.014 0.002 TYR A 508 PHE 0.015 0.002 PHE L 71 TRP 0.012 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 3284) covalent geometry : angle 0.71566 / 0.36 ( 4465) SS BOND : bond 0.00338 / 0.17 ( 5) SS BOND : angle 1.28681 / 0.80 ( 10) hydrogen bonds : bond 0.04747 / 3.17 ( 100) hydrogen bonds : angle 7.62975 / 5.31 ( 255) link_BETA1-4 : bond 0.01150 / 0.56 ( 2) link_BETA1-4 : angle 2.71688 / 1.37 ( 6) link_BETA1-6 : bond 0.00173 / 0.09 ( 1) link_BETA1-6 : angle 1.91283 / 1.00 ( 3) link_NAG-ASN : bond 0.00430 / 0.23 ( 1) link_NAG-ASN : angle 2.16924 / 1.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.118 Fit side-chains REVERT: A 442 ASP cc_start: 0.7944 (m-30) cc_final: 0.7656 (m-30) REVERT: L 105 GLU cc_start: 0.4911 (tp30) cc_final: 0.4671 (tp30) outliers start: 6 outliers final: 3 residues processed: 72 average time/residue: 0.0607 time to fit residues: 5.4077 Evaluate side-chains 65 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain L residue 40 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.0030 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 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 = 0.3851 r_free = 0.3851 target = 0.130329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108969 restraints weight = 5781.690| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.16 r_work: 0.3438 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3293 Z= 0.141 Angle : 0.691 13.293 4487 Z= 0.333 Chirality : 0.045 0.173 493 Planarity : 0.005 0.051 565 Dihedral : 5.195 17.727 443 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.18 % Allowed : 11.56 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.71 (0.41), residues: 394 helix: -1.64 (0.95), residues: 34 sheet: 0.18 (0.41), residues: 146 loop : -0.68 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 65 TYR 0.010 0.001 TYR H 102 PHE 0.023 0.002 PHE A 497 TRP 0.012 0.001 TRP A 436 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 3284) covalent geometry : angle 0.68031 / 0.33 ( 4465) SS BOND : bond 0.00247 / 0.13 ( 5) SS BOND : angle 1.07537 / 0.67 ( 10) hydrogen bonds : bond 0.03933 / 2.65 ( 100) hydrogen bonds : angle 6.96450 / 4.85 ( 255) link_BETA1-4 : bond 0.00958 / 0.47 ( 2) link_BETA1-4 : angle 2.48085 / 1.25 ( 6) link_BETA1-6 : bond 0.00364 / 0.19 ( 1) link_BETA1-6 : angle 1.92113 / 1.02 ( 3) link_NAG-ASN : bond 0.00380 / 0.20 ( 1) link_NAG-ASN : angle 2.10803 / 1.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.110 Fit side-chains REVERT: A 403 ARG cc_start: 0.7978 (ptm160) cc_final: 0.7545 (ptm-80) REVERT: A 406 GLU cc_start: 0.8107 (mp0) cc_final: 0.7757 (mp0) REVERT: A 442 ASP cc_start: 0.7932 (m-30) cc_final: 0.7480 (m-30) REVERT: H 112 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7041 (mp10) REVERT: L 86 TYR cc_start: 0.7038 (m-80) cc_final: 0.6817 (m-80) REVERT: L 105 GLU cc_start: 0.5210 (tp30) cc_final: 0.4906 (tp30) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 0.0661 time to fit residues: 6.2259 Evaluate side-chains 73 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 40 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 5 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 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 = 0.3841 r_free = 0.3841 target = 0.129704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107636 restraints weight = 5868.342| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.22 r_work: 0.3411 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3293 Z= 0.175 Angle : 0.683 11.389 4487 Z= 0.334 Chirality : 0.045 0.170 493 Planarity : 0.005 0.051 565 Dihedral : 5.184 17.221 443 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.47 % Allowed : 12.14 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.73 (0.41), residues: 394 helix: -1.92 (0.89), residues: 34 sheet: 0.22 (0.41), residues: 149 loop : -0.71 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 457 TYR 0.021 0.001 TYR H 80 PHE 0.014 0.002 PHE A 497 TRP 0.011 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 3284) covalent geometry : angle 0.67255 / 0.33 ( 4465) SS BOND : bond 0.00313 / 0.16 ( 5) SS BOND : angle 1.14749 / 0.72 ( 10) hydrogen bonds : bond 0.03795 / 2.55 ( 100) hydrogen bonds : angle 6.69166 / 4.65 ( 255) link_BETA1-4 : bond 0.00861 / 0.43 ( 2) link_BETA1-4 : angle 2.32843 / 1.19 ( 6) link_BETA1-6 : bond 0.00312 / 0.16 ( 1) link_BETA1-6 : angle 2.09149 / 1.11 ( 3) link_NAG-ASN : bond 0.00439 / 0.23 ( 1) link_NAG-ASN : angle 2.10847 / 1.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.131 Fit side-chains REVERT: A 403 ARG cc_start: 0.8069 (ptm160) cc_final: 0.7426 (ptm-80) REVERT: A 406 GLU cc_start: 0.8155 (mp0) cc_final: 0.7458 (mp0) REVERT: A 442 ASP cc_start: 0.7896 (m-30) cc_final: 0.7312 (m-30) REVERT: H 90 ASP cc_start: 0.6791 (t70) cc_final: 0.6580 (t0) REVERT: H 102 TYR cc_start: 0.8570 (m-80) cc_final: 0.8347 (m-80) REVERT: H 112 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: L 105 GLU cc_start: 0.5068 (tp30) cc_final: 0.4744 (tp30) outliers start: 12 outliers final: 7 residues processed: 73 average time/residue: 0.0543 time to fit residues: 5.0078 Evaluate side-chains 74 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 40 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 5 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 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 = 0.3842 r_free = 0.3842 target = 0.130507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109028 restraints weight = 5798.444| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.17 r_work: 0.3439 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3293 Z= 0.132 Angle : 0.655 11.132 4487 Z= 0.318 Chirality : 0.044 0.165 493 Planarity : 0.005 0.051 565 Dihedral : 4.978 17.580 443 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.18 % Allowed : 13.58 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.68 (0.42), residues: 394 helix: -2.17 (0.77), residues: 40 sheet: 0.33 (0.41), residues: 154 loop : -0.64 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 65 TYR 0.008 0.001 TYR A 369 PHE 0.011 0.001 PHE A 497 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 3284) covalent geometry : angle 0.64540 / 0.32 ( 4465) SS BOND : bond 0.00264 / 0.14 ( 5) SS BOND : angle 1.07600 / 0.69 ( 10) hydrogen bonds : bond 0.03418 / 2.30 ( 100) hydrogen bonds : angle 6.38975 / 4.43 ( 255) link_BETA1-4 : bond 0.00892 / 0.44 ( 2) link_BETA1-4 : angle 2.21215 / 1.12 ( 6) link_BETA1-6 : bond 0.00279 / 0.15 ( 1) link_BETA1-6 : angle 1.93145 / 1.02 ( 3) link_NAG-ASN : bond 0.00322 / 0.17 ( 1) link_NAG-ASN : angle 2.17400 / 1.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.139 Fit side-chains REVERT: A 403 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7207 (ptm-80) REVERT: A 406 GLU cc_start: 0.8237 (mp0) cc_final: 0.7524 (mp0) REVERT: A 442 ASP cc_start: 0.7928 (m-30) cc_final: 0.7344 (m-30) REVERT: H 46 GLU cc_start: 0.7966 (pt0) cc_final: 0.7719 (pt0) REVERT: H 112 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: L 105 GLU cc_start: 0.5377 (tp30) cc_final: 0.5046 (tp30) outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 0.0735 time to fit residues: 6.5865 Evaluate side-chains 74 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 40 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 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 = 0.3837 r_free = 0.3837 target = 0.129439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.107372 restraints weight = 5838.385| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.21 r_work: 0.3412 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3293 Z= 0.177 Angle : 0.667 11.126 4487 Z= 0.327 Chirality : 0.044 0.156 493 Planarity : 0.005 0.053 565 Dihedral : 5.033 17.897 443 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.47 % Allowed : 15.61 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.69 (0.42), residues: 394 helix: -2.29 (0.75), residues: 40 sheet: 0.44 (0.42), residues: 148 loop : -0.70 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 65 TYR 0.017 0.001 TYR H 80 PHE 0.012 0.002 PHE A 497 TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 3284) covalent geometry : angle 0.65695 / 0.32 ( 4465) SS BOND : bond 0.00185 / 0.10 ( 5) SS BOND : angle 1.22552 / 0.78 ( 10) hydrogen bonds : bond 0.03611 / 2.43 ( 100) hydrogen bonds : angle 6.31423 / 4.38 ( 255) link_BETA1-4 : bond 0.00792 / 0.39 ( 2) link_BETA1-4 : angle 2.14105 / 1.10 ( 6) link_BETA1-6 : bond 0.00438 / 0.23 ( 1) link_BETA1-6 : angle 2.09248 / 1.10 ( 3) link_NAG-ASN : bond 0.00399 / 0.21 ( 1) link_NAG-ASN : angle 2.15923 / 1.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.123 Fit side-chains REVERT: A 403 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7376 (ptm-80) REVERT: A 406 GLU cc_start: 0.8224 (mp0) cc_final: 0.7242 (mp0) REVERT: A 442 ASP cc_start: 0.7876 (m-30) cc_final: 0.7344 (m-30) REVERT: H 46 GLU cc_start: 0.8016 (pt0) cc_final: 0.7761 (pt0) REVERT: H 112 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7164 (mp10) REVERT: L 105 GLU cc_start: 0.5196 (tp30) cc_final: 0.4863 (tp30) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.0579 time to fit residues: 5.0455 Evaluate side-chains 73 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 40 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 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 = 0.3847 r_free = 0.3847 target = 0.130121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.108056 restraints weight = 6046.742| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.26 r_work: 0.3422 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3293 Z= 0.140 Angle : 0.636 9.530 4487 Z= 0.314 Chirality : 0.044 0.165 493 Planarity : 0.004 0.056 565 Dihedral : 4.886 17.833 443 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.47 % Allowed : 16.76 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.84 (0.42), residues: 394 helix: -2.40 (0.74), residues: 40 sheet: 0.19 (0.41), residues: 160 loop : -0.71 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 65 TYR 0.013 0.001 TYR A 369 PHE 0.010 0.001 PHE A 497 TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 3284) covalent geometry : angle 0.62649 / 0.31 ( 4465) SS BOND : bond 0.00244 / 0.13 ( 5) SS BOND : angle 1.15573 / 0.74 ( 10) hydrogen bonds : bond 0.03308 / 2.24 ( 100) hydrogen bonds : angle 6.19448 / 4.30 ( 255) link_BETA1-4 : bond 0.00769 / 0.38 ( 2) link_BETA1-4 : angle 2.11213 / 1.08 ( 6) link_BETA1-6 : bond 0.00418 / 0.22 ( 1) link_BETA1-6 : angle 1.91636 / 1.01 ( 3) link_NAG-ASN : bond 0.00331 / 0.17 ( 1) link_NAG-ASN : angle 2.15178 / 1.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.146 Fit side-chains REVERT: A 403 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7201 (ptm-80) REVERT: A 406 GLU cc_start: 0.8292 (mp0) cc_final: 0.7291 (mp0) REVERT: A 442 ASP cc_start: 0.7844 (m-30) cc_final: 0.7395 (m-30) REVERT: H 46 GLU cc_start: 0.8031 (pt0) cc_final: 0.7754 (pt0) REVERT: H 112 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: L 105 GLU cc_start: 0.5172 (tp30) cc_final: 0.4841 (tp30) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.0672 time to fit residues: 5.7304 Evaluate side-chains 73 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.130559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108192 restraints weight = 6084.491| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.22 r_work: 0.3416 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3293 Z= 0.172 Angle : 0.663 9.114 4487 Z= 0.329 Chirality : 0.045 0.169 493 Planarity : 0.005 0.056 565 Dihedral : 4.913 16.917 443 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.91 % Allowed : 16.47 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.83 (0.43), residues: 394 helix: -2.24 (0.77), residues: 39 sheet: 0.24 (0.42), residues: 160 loop : -0.79 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 65 TYR 0.019 0.001 TYR H 80 PHE 0.010 0.001 PHE A 497 TRP 0.013 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 3284) covalent geometry : angle 0.64724 / 0.32 ( 4465) SS BOND : bond 0.00404 / 0.20 ( 5) SS BOND : angle 2.19817 / 1.29 ( 10) hydrogen bonds : bond 0.03581 / 2.42 ( 100) hydrogen bonds : angle 6.30216 / 4.43 ( 255) link_BETA1-4 : bond 0.00783 / 0.38 ( 2) link_BETA1-4 : angle 2.08136 / 1.08 ( 6) link_BETA1-6 : bond 0.00442 / 0.23 ( 1) link_BETA1-6 : angle 2.05313 / 1.08 ( 3) link_NAG-ASN : bond 0.00398 / 0.21 ( 1) link_NAG-ASN : angle 2.10980 / 1.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.130 Fit side-chains REVERT: A 403 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7736 (ptm-80) REVERT: A 442 ASP cc_start: 0.7902 (m-30) cc_final: 0.7391 (m-30) REVERT: H 46 GLU cc_start: 0.8031 (pt0) cc_final: 0.7788 (pt0) REVERT: H 112 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7126 (mp10) REVERT: L 105 GLU cc_start: 0.5244 (tp30) cc_final: 0.4934 (tp30) outliers start: 17 outliers final: 12 residues processed: 71 average time/residue: 0.0497 time to fit residues: 4.3932 Evaluate side-chains 77 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 24 optimal weight: 0.0030 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.131398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.109268 restraints weight = 5987.912| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.20 r_work: 0.3444 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3293 Z= 0.119 Angle : 0.637 8.978 4487 Z= 0.317 Chirality : 0.044 0.183 493 Planarity : 0.004 0.056 565 Dihedral : 4.744 18.638 443 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.18 % Allowed : 17.92 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.43), residues: 394 helix: -2.36 (0.75), residues: 40 sheet: 0.22 (0.41), residues: 160 loop : -0.70 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 65 TYR 0.013 0.001 TYR A 369 PHE 0.009 0.001 PHE A 497 TRP 0.011 0.001 TRP A 436 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 3284) covalent geometry : angle 0.62509 / 0.31 ( 4465) SS BOND : bond 0.00207 / 0.11 ( 5) SS BOND : angle 1.67125 / 1.00 ( 10) hydrogen bonds : bond 0.03233 / 2.17 ( 100) hydrogen bonds : angle 6.21951 / 4.35 ( 255) link_BETA1-4 : bond 0.00803 / 0.39 ( 2) link_BETA1-4 : angle 2.07166 / 1.04 ( 6) link_BETA1-6 : bond 0.00207 / 0.11 ( 1) link_BETA1-6 : angle 1.93510 / 1.01 ( 3) link_NAG-ASN : bond 0.00319 / 0.17 ( 1) link_NAG-ASN : angle 2.15074 / 1.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.090 Fit side-chains REVERT: A 403 ARG cc_start: 0.8364 (ptm160) cc_final: 0.7709 (ptm-80) REVERT: A 406 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7979 (mm-30) REVERT: A 442 ASP cc_start: 0.7877 (m-30) cc_final: 0.7452 (m-30) REVERT: H 46 GLU cc_start: 0.7989 (pt0) cc_final: 0.7767 (pt0) REVERT: H 112 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7163 (mp10) REVERT: L 105 GLU cc_start: 0.5220 (tp30) cc_final: 0.4874 (tp30) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.0509 time to fit residues: 4.3298 Evaluate side-chains 70 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.0670 chunk 8 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.130590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108443 restraints weight = 5958.052| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.18 r_work: 0.3433 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3293 Z= 0.142 Angle : 0.644 8.528 4487 Z= 0.322 Chirality : 0.044 0.190 493 Planarity : 0.005 0.056 565 Dihedral : 4.754 19.064 443 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.47 % Allowed : 17.92 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.82 (0.43), residues: 394 helix: -2.28 (0.76), residues: 39 sheet: 0.24 (0.42), residues: 160 loop : -0.76 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 65 TYR 0.013 0.001 TYR A 369 PHE 0.009 0.001 PHE A 497 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 3284) covalent geometry : angle 0.63257 / 0.32 ( 4465) SS BOND : bond 0.00180 / 0.10 ( 5) SS BOND : angle 1.66345 / 1.01 ( 10) hydrogen bonds : bond 0.03276 / 2.21 ( 100) hydrogen bonds : angle 6.15531 / 4.32 ( 255) link_BETA1-4 : bond 0.00792 / 0.39 ( 2) link_BETA1-4 : angle 1.99332 / 1.02 ( 6) link_BETA1-6 : bond 0.00362 / 0.19 ( 1) link_BETA1-6 : angle 1.98206 / 1.03 ( 3) link_NAG-ASN : bond 0.00388 / 0.20 ( 1) link_NAG-ASN : angle 2.09736 / 1.22 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.124 Fit side-chains REVERT: A 403 ARG cc_start: 0.8318 (ptm160) cc_final: 0.7623 (ptm-80) REVERT: A 406 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8023 (mm-30) REVERT: A 442 ASP cc_start: 0.7900 (m-30) cc_final: 0.7452 (m-30) REVERT: H 46 GLU cc_start: 0.7932 (pt0) cc_final: 0.7700 (pt0) REVERT: H 112 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: L 105 GLU cc_start: 0.5197 (tp30) cc_final: 0.4901 (tp30) outliers start: 12 outliers final: 10 residues processed: 67 average time/residue: 0.0628 time to fit residues: 5.2301 Evaluate side-chains 71 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.0030 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.131878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109924 restraints weight = 6023.249| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.24 r_work: 0.3448 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3293 Z= 0.106 Angle : 0.628 9.024 4487 Z= 0.313 Chirality : 0.044 0.196 493 Planarity : 0.004 0.056 565 Dihedral : 4.596 18.033 443 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.47 % Allowed : 17.63 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.79 (0.43), residues: 394 helix: -2.45 (0.72), residues: 40 sheet: 0.26 (0.42), residues: 160 loop : -0.70 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 65 TYR 0.021 0.001 TYR H 80 PHE 0.009 0.001 PHE A 497 TRP 0.011 0.001 TRP A 436 HIS 0.001 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 3284) covalent geometry : angle 0.61774 / 0.31 ( 4465) SS BOND : bond 0.00206 / 0.12 ( 5) SS BOND : angle 1.36673 / 0.83 ( 10) hydrogen bonds : bond 0.03005 / 2.02 ( 100) hydrogen bonds : angle 6.13649 / 4.29 ( 255) link_BETA1-4 : bond 0.00905 / 0.44 ( 2) link_BETA1-4 : angle 1.98122 / 1.00 ( 6) link_BETA1-6 : bond 0.00153 / 0.08 ( 1) link_BETA1-6 : angle 1.82417 / 0.94 ( 3) link_NAG-ASN : bond 0.00307 / 0.16 ( 1) link_NAG-ASN : angle 2.14542 / 1.26 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 856.46 seconds wall clock time: 15 minutes 25.60 seconds (925.60 seconds total)