Starting phenix.real_space_refine on Wed Jul 1 22:53:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zr8_14886/07_2026/7zr8_14886.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr8_14886/07_2026/7zr8_14886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zr8_14886/07_2026/7zr8_14886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr8_14886/07_2026/7zr8_14886.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zr8_14886/07_2026/7zr8_14886.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zr8_14886/07_2026/7zr8_14886.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zr8_14886/07_2026/7zr8_14886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr8_14886/07_2026/7zr8_14886.cif" } resolution = 3.7 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= 0.012 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 2346 2.51 5 N 623 2.21 5 O 706 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3693 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1945 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 13, 'TRANS': 231} Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.87, per 1000 atoms: 0.24 Number of scatterers: 3693 At special positions: 0 Unit cell: (68.06, 75.53, 111.22, 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 706 8.00 N 623 7.00 C 2346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " 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 NAG-ASN " NAG A1301 " - " ASN A 340 " Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 119.6 milliseconds 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 866 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 12 sheets defined 9.6% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.601A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.017A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.371A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.137A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.714A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 323 removed outlier: 7.131A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 323 removed outlier: 7.131A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.569A pdb=" N LYS A 353 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.794A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA6, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.926A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.926A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY H 100 " --> pdb=" O PHE H 105 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE H 105 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.530A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.339A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 112 hydrogen bonds defined for protein. 252 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: 0.53 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1178 1.34 - 1.46: 930 1.46 - 1.58: 1653 1.58 - 1.69: 0 1.69 - 1.81: 23 Bond restraints: 3784 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C2 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.439 1.455 -0.016 2.00e-02 2.50e+03 6.08e-01 bond pdb=" C4 NAG A1301 " pdb=" O4 NAG A1301 " ideal model delta sigma weight residual 1.409 1.423 -0.014 2.00e-02 2.50e+03 4.82e-01 ... (remaining 3779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 4994 1.15 - 2.31: 101 2.31 - 3.46: 37 3.46 - 4.61: 4 4.61 - 5.77: 1 Bond angle restraints: 5137 Sorted by residual: angle pdb=" N ILE L 29 " pdb=" CA ILE L 29 " pdb=" C ILE L 29 " ideal model delta sigma weight residual 111.77 109.00 2.77 1.04e+00 9.25e-01 7.10e+00 angle pdb=" C ALA A 517 " pdb=" N PRO A 518 " pdb=" CA PRO A 518 " ideal model delta sigma weight residual 121.65 119.16 2.49 1.01e+00 9.80e-01 6.07e+00 angle pdb=" N ASP H 103 " pdb=" CA ASP H 103 " pdb=" CB ASP H 103 " ideal model delta sigma weight residual 113.65 110.44 3.21 1.47e+00 4.63e-01 4.78e+00 angle pdb=" N TYR L 94 " pdb=" CA TYR L 94 " pdb=" C TYR L 94 " ideal model delta sigma weight residual 112.97 110.97 2.00 1.06e+00 8.90e-01 3.57e+00 angle pdb=" C ASP L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.02 -3.48 1.91e+00 2.74e-01 3.32e+00 ... (remaining 5132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.18: 2026 10.18 - 20.36: 143 20.36 - 30.54: 47 30.54 - 40.72: 13 40.72 - 50.90: 5 Dihedral angle restraints: 2234 sinusoidal: 872 harmonic: 1362 Sorted by residual: dihedral pdb=" CA LEU L 33 " pdb=" CB LEU L 33 " pdb=" CG LEU L 33 " pdb=" CD1 LEU L 33 " ideal model delta sinusoidal sigma weight residual 180.00 129.10 50.90 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA PRO A 524 " pdb=" C PRO A 524 " pdb=" N LYS A 525 " pdb=" CA LYS A 525 " ideal model delta harmonic sigma weight residual 180.00 165.32 14.68 0 5.00e+00 4.00e-02 8.62e+00 dihedral pdb=" N TYR A 498 " pdb=" CA TYR A 498 " pdb=" CB TYR A 498 " pdb=" CG TYR A 498 " ideal model delta sinusoidal sigma weight residual -60.00 -108.10 48.10 3 1.50e+01 4.44e-03 8.59e+00 ... (remaining 2231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 340 0.030 - 0.059: 142 0.059 - 0.089: 30 0.089 - 0.118: 42 0.118 - 0.148: 4 Chirality restraints: 558 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE A 399 " pdb=" N ILE A 399 " pdb=" C ILE A 399 " pdb=" CB ILE A 399 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 555 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 95 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.83e+00 pdb=" N PRO L 96 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 326 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 327 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 557 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO A 558 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 558 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 558 " -0.014 5.00e-02 4.00e+02 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 174 2.73 - 3.27: 3512 3.27 - 3.81: 5835 3.81 - 4.36: 7174 4.36 - 4.90: 12818 Nonbonded interactions: 29513 Sorted by model distance: nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.181 3.040 nonbonded pdb=" OG1 THR H 33 " pdb=" OG SER H 99 " model vdw 2.223 3.040 nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 103 " model vdw 2.255 3.040 nonbonded pdb=" O LYS H 13 " pdb=" OG SER H 16 " model vdw 2.281 3.040 nonbonded pdb=" O GLN L 90 " pdb=" N GLU L 92 " model vdw 2.291 3.120 ... (remaining 29508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.000 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.510 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: 10.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.003 0.028 3791 Z= 0.124 Angle : 0.466 5.767 5152 Z= 0.249 Chirality : 0.042 0.148 558 Planarity : 0.004 0.049 663 Dihedral : 8.450 50.903 1350 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.74 % Allowed : 3.71 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.94 (0.42), residues: 465 helix: -3.12 (0.74), residues: 33 sheet: -0.75 (0.46), residues: 156 loop : -0.08 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 506 TYR 0.009 0.001 TYR L 91 PHE 0.009 0.001 PHE A 426 TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 3784) covalent geometry : angle 0.46498 / 0.25 ( 5137) SS BOND : bond 0.00113 / 0.07 ( 6) SS BOND : angle 0.33517 / 0.18 ( 12) hydrogen bonds : bond 0.24152 / 17.06 ( 106) hydrogen bonds : angle 11.62971 / 7.93 ( 252) link_NAG-ASN : bond 0.00039 / 0.02 ( 1) link_NAG-ASN : angle 1.33788 / 0.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9035 (tp) cc_final: 0.8645 (pt) REVERT: A 343 ARG cc_start: 0.9345 (mtt-85) cc_final: 0.9013 (ttm-80) REVERT: A 511 SER cc_start: 0.9440 (m) cc_final: 0.9192 (t) REVERT: A 532 LYS cc_start: 0.8724 (mttt) cc_final: 0.8496 (mttp) outliers start: 3 outliers final: 1 residues processed: 89 average time/residue: 0.0890 time to fit residues: 9.4087 Evaluate side-chains 67 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 ASN A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.157194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130267 restraints weight = 4450.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131192 restraints weight = 4026.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131592 restraints weight = 3732.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132201 restraints weight = 3571.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132201 restraints weight = 3416.553| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3791 Z= 0.207 Angle : 0.552 4.809 5152 Z= 0.299 Chirality : 0.045 0.157 558 Planarity : 0.005 0.045 663 Dihedral : 4.724 44.850 520 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.97 % Allowed : 10.89 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.42), residues: 465 helix: -3.20 (0.92), residues: 28 sheet: -0.76 (0.45), residues: 153 loop : 0.01 (0.41), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 50 TYR 0.021 0.002 TYR L 91 PHE 0.012 0.001 PHE A 426 TRP 0.008 0.001 TRP H 108 HIS 0.002 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 ( 3784) covalent geometry : angle 0.55050 / 0.30 ( 5137) SS BOND : bond 0.00316 / 0.20 ( 6) SS BOND : angle 0.67787 / 0.35 ( 12) hydrogen bonds : bond 0.04679 / 3.25 ( 106) hydrogen bonds : angle 7.70605 / 5.29 ( 252) link_NAG-ASN : bond 0.00028 / 0.01 ( 1) link_NAG-ASN : angle 1.54841 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9111 (tp) cc_final: 0.8816 (pt) REVERT: A 343 ARG cc_start: 0.9297 (mtt-85) cc_final: 0.9029 (ttm-80) REVERT: L 38 GLN cc_start: 0.9172 (tt0) cc_final: 0.8825 (tt0) outliers start: 12 outliers final: 8 residues processed: 76 average time/residue: 0.0963 time to fit residues: 8.6367 Evaluate side-chains 74 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 10 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 ASN A 539 ASN L 6 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.160533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.134742 restraints weight = 4339.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135188 restraints weight = 3978.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.136044 restraints weight = 3771.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.136044 restraints weight = 3542.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.136082 restraints weight = 3540.954| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3791 Z= 0.165 Angle : 0.520 5.842 5152 Z= 0.277 Chirality : 0.045 0.153 558 Planarity : 0.004 0.042 663 Dihedral : 4.813 51.047 520 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.97 % Allowed : 12.62 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.91 (0.41), residues: 465 helix: -3.21 (0.89), residues: 28 sheet: -0.84 (0.43), residues: 153 loop : -0.05 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 325 TYR 0.017 0.001 TYR L 91 PHE 0.009 0.001 PHE A 426 TRP 0.009 0.001 TRP A 433 HIS 0.001 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 3784) covalent geometry : angle 0.51824 / 0.28 ( 5137) SS BOND : bond 0.00221 / 0.13 ( 6) SS BOND : angle 0.70731 / 0.35 ( 12) hydrogen bonds : bond 0.03636 / 2.55 ( 106) hydrogen bonds : angle 6.85628 / 4.69 ( 252) link_NAG-ASN : bond 0.00032 / 0.02 ( 1) link_NAG-ASN : angle 1.45275 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9104 (tp) cc_final: 0.8845 (pt) REVERT: L 38 GLN cc_start: 0.9132 (tt0) cc_final: 0.8851 (tt0) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.0891 time to fit residues: 7.7817 Evaluate side-chains 71 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN ** L 90 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 = 0.3755 r_free = 0.3755 target = 0.159012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.134667 restraints weight = 4368.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134227 restraints weight = 3949.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134189 restraints weight = 3771.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134216 restraints weight = 3685.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134291 restraints weight = 3655.109| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3791 Z= 0.225 Angle : 0.552 5.685 5152 Z= 0.296 Chirality : 0.045 0.161 558 Planarity : 0.004 0.042 663 Dihedral : 5.047 55.984 520 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.71 % Allowed : 14.11 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.16 (0.40), residues: 465 helix: -3.19 (0.88), residues: 29 sheet: -1.01 (0.42), residues: 153 loop : -0.23 (0.39), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 454 TYR 0.017 0.002 TYR L 91 PHE 0.013 0.001 PHE A 426 TRP 0.010 0.002 TRP A 433 HIS 0.002 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 ( 3784) covalent geometry : angle 0.54975 / 0.30 ( 5137) SS BOND : bond 0.00223 / 0.13 ( 6) SS BOND : angle 0.92929 / 0.46 ( 12) hydrogen bonds : bond 0.03582 / 2.51 ( 106) hydrogen bonds : angle 6.76514 / 4.62 ( 252) link_NAG-ASN : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : angle 1.77420 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9106 (tp) cc_final: 0.8892 (pt) outliers start: 15 outliers final: 14 residues processed: 74 average time/residue: 0.0831 time to fit residues: 7.4516 Evaluate side-chains 75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN ** L 90 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 = 0.3723 r_free = 0.3723 target = 0.156402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129383 restraints weight = 4367.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129798 restraints weight = 3925.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130763 restraints weight = 3746.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131542 restraints weight = 3524.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131543 restraints weight = 3366.327| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3791 Z= 0.191 Angle : 0.544 6.356 5152 Z= 0.291 Chirality : 0.045 0.153 558 Planarity : 0.004 0.040 663 Dihedral : 5.080 59.591 520 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.21 % Allowed : 13.61 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.26 (0.40), residues: 465 helix: -3.09 (0.88), residues: 29 sheet: -1.13 (0.42), residues: 154 loop : -0.29 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 325 TYR 0.015 0.001 TYR L 91 PHE 0.010 0.001 PHE A 426 TRP 0.010 0.002 TRP A 433 HIS 0.001 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 3784) covalent geometry : angle 0.54120 / 0.29 ( 5137) SS BOND : bond 0.00232 / 0.14 ( 6) SS BOND : angle 0.91508 / 0.46 ( 12) hydrogen bonds : bond 0.03319 / 2.34 ( 106) hydrogen bonds : angle 6.54577 / 4.47 ( 252) link_NAG-ASN : bond 0.00005 / 0.00 ( 1) link_NAG-ASN : angle 1.68336 / 0.95 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6232 (ptp90) outliers start: 17 outliers final: 14 residues processed: 74 average time/residue: 0.0667 time to fit residues: 6.0375 Evaluate side-chains 77 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN ** L 90 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 = 0.3726 r_free = 0.3726 target = 0.156453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131622 restraints weight = 4432.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.130931 restraints weight = 5239.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131041 restraints weight = 5165.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131190 restraints weight = 4886.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.131540 restraints weight = 4449.911| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3791 Z= 0.214 Angle : 0.557 6.823 5152 Z= 0.299 Chirality : 0.045 0.156 558 Planarity : 0.004 0.041 663 Dihedral : 5.115 57.559 520 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.94 % Allowed : 13.86 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.34 (0.40), residues: 465 helix: -3.05 (0.89), residues: 29 sheet: -1.21 (0.41), residues: 155 loop : -0.33 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 325 TYR 0.015 0.001 TYR L 91 PHE 0.011 0.001 PHE A 426 TRP 0.010 0.002 TRP A 433 HIS 0.002 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 ( 3784) covalent geometry : angle 0.55410 / 0.30 ( 5137) SS BOND : bond 0.00217 / 0.12 ( 6) SS BOND : angle 0.94236 / 0.47 ( 12) hydrogen bonds : bond 0.03314 / 2.32 ( 106) hydrogen bonds : angle 6.53650 / 4.47 ( 252) link_NAG-ASN : bond 0.00020 / 0.01 ( 1) link_NAG-ASN : angle 1.79409 / 1.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8804 (mt) REVERT: A 389 PHE cc_start: 0.8838 (m-80) cc_final: 0.8593 (m-80) REVERT: A 463 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7179 (ttp-170) REVERT: A 564 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6282 (ptp90) REVERT: H 112 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8382 (t) outliers start: 24 outliers final: 17 residues processed: 73 average time/residue: 0.0652 time to fit residues: 5.8642 Evaluate side-chains 77 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 6 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN ** L 90 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 = 0.3747 r_free = 0.3747 target = 0.158397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131750 restraints weight = 4465.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132748 restraints weight = 3985.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132748 restraints weight = 3674.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132748 restraints weight = 3674.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132748 restraints weight = 3674.794| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3791 Z= 0.160 Angle : 0.533 7.984 5152 Z= 0.285 Chirality : 0.044 0.151 558 Planarity : 0.004 0.040 663 Dihedral : 4.826 51.918 520 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.45 % Allowed : 14.60 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.40), residues: 465 helix: -2.96 (0.87), residues: 29 sheet: -1.09 (0.41), residues: 154 loop : -0.31 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 325 TYR 0.014 0.001 TYR A 486 PHE 0.010 0.001 PHE A 540 TRP 0.011 0.002 TRP A 433 HIS 0.001 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 3784) covalent geometry : angle 0.53083 / 0.28 ( 5137) SS BOND : bond 0.00232 / 0.13 ( 6) SS BOND : angle 0.88305 / 0.44 ( 12) hydrogen bonds : bond 0.03067 / 2.15 ( 106) hydrogen bonds : angle 6.28973 / 4.29 ( 252) link_NAG-ASN : bond 0.00012 / 0.01 ( 1) link_NAG-ASN : angle 1.57699 / 0.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8845 (mt) REVERT: A 389 PHE cc_start: 0.8823 (m-80) cc_final: 0.8594 (m-80) REVERT: A 564 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6297 (ptp90) REVERT: H 112 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8278 (t) outliers start: 22 outliers final: 16 residues processed: 72 average time/residue: 0.0707 time to fit residues: 6.3519 Evaluate side-chains 74 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 1 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN ** L 90 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 = 0.3737 r_free = 0.3737 target = 0.157640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.131698 restraints weight = 4330.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132746 restraints weight = 3889.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.133240 restraints weight = 3598.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.133243 restraints weight = 3413.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.133243 restraints weight = 3411.935| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3791 Z= 0.158 Angle : 0.543 8.574 5152 Z= 0.291 Chirality : 0.045 0.151 558 Planarity : 0.004 0.040 663 Dihedral : 4.663 45.803 520 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.70 % Allowed : 15.10 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.19 (0.40), residues: 465 helix: -2.86 (0.89), residues: 29 sheet: -1.01 (0.41), residues: 154 loop : -0.32 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 325 TYR 0.014 0.001 TYR A 486 PHE 0.009 0.001 PHE A 540 TRP 0.010 0.002 TRP A 433 HIS 0.002 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 3784) covalent geometry : angle 0.54098 / 0.29 ( 5137) SS BOND : bond 0.00222 / 0.12 ( 6) SS BOND : angle 0.91088 / 0.46 ( 12) hydrogen bonds : bond 0.03028 / 2.12 ( 106) hydrogen bonds : angle 6.18365 / 4.20 ( 252) link_NAG-ASN : bond 0.00030 / 0.02 ( 1) link_NAG-ASN : angle 1.52768 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.9077 (mt) cc_final: 0.8845 (mt) REVERT: A 389 PHE cc_start: 0.8823 (m-80) cc_final: 0.8601 (m-80) REVERT: A 564 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6290 (ptp90) REVERT: H 112 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8280 (t) outliers start: 19 outliers final: 16 residues processed: 65 average time/residue: 0.0553 time to fit residues: 4.5874 Evaluate side-chains 72 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 0.0060 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 ASN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.158349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132525 restraints weight = 4338.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.133451 restraints weight = 3892.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133874 restraints weight = 3593.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133941 restraints weight = 3426.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133944 restraints weight = 3414.527| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3791 Z= 0.147 Angle : 0.537 9.513 5152 Z= 0.288 Chirality : 0.045 0.150 558 Planarity : 0.004 0.040 663 Dihedral : 4.455 39.305 520 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.70 % Allowed : 15.10 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.12 (0.40), residues: 465 helix: -2.75 (0.92), residues: 29 sheet: -0.91 (0.41), residues: 154 loop : -0.30 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 325 TYR 0.014 0.001 TYR A 486 PHE 0.009 0.001 PHE A 540 TRP 0.010 0.001 TRP A 433 HIS 0.001 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 3784) covalent geometry : angle 0.53456 / 0.29 ( 5137) SS BOND : bond 0.00225 / 0.13 ( 6) SS BOND : angle 0.88284 / 0.45 ( 12) hydrogen bonds : bond 0.02980 / 2.09 ( 106) hydrogen bonds : angle 6.02209 / 4.08 ( 252) link_NAG-ASN : bond 0.00039 / 0.02 ( 1) link_NAG-ASN : angle 1.46314 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.9035 (mt) cc_final: 0.8798 (mt) REVERT: A 389 PHE cc_start: 0.8843 (m-80) cc_final: 0.8607 (m-80) REVERT: A 564 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6296 (ptp90) REVERT: H 112 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8314 (t) outliers start: 19 outliers final: 15 residues processed: 65 average time/residue: 0.0485 time to fit residues: 4.1355 Evaluate side-chains 70 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 9 optimal weight: 0.0170 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.0470 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.0370 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.0170 overall best weight: 0.0430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN ** L 90 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 = 0.3801 r_free = 0.3801 target = 0.163719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.138972 restraints weight = 4366.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.140051 restraints weight = 3828.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.140051 restraints weight = 3486.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.141086 restraints weight = 3486.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.141086 restraints weight = 3265.952| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 3791 Z= 0.095 Angle : 0.517 9.261 5152 Z= 0.281 Chirality : 0.044 0.141 558 Planarity : 0.004 0.039 663 Dihedral : 4.033 27.686 520 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.23 % Allowed : 17.57 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.41), residues: 465 helix: -2.75 (0.91), residues: 29 sheet: -0.63 (0.42), residues: 154 loop : -0.12 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 343 TYR 0.014 0.001 TYR A 486 PHE 0.009 0.001 PHE A 540 TRP 0.015 0.002 TRP A 433 HIS 0.001 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 3784) covalent geometry : angle 0.51515 / 0.28 ( 5137) SS BOND : bond 0.00294 / 0.18 ( 6) SS BOND : angle 0.84022 / 0.42 ( 12) hydrogen bonds : bond 0.02757 / 1.98 ( 106) hydrogen bonds : angle 5.67113 / 3.84 ( 252) link_NAG-ASN : bond 0.00117 / 0.06 ( 1) link_NAG-ASN : angle 1.09832 / 0.63 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.8985 (mt) cc_final: 0.8773 (mt) REVERT: A 564 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6267 (ptp90) REVERT: H 34 ILE cc_start: 0.9080 (mm) cc_final: 0.8859 (mt) REVERT: H 112 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8235 (t) outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 0.0785 time to fit residues: 6.3886 Evaluate side-chains 62 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.0570 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN ** L 90 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 = 0.3824 r_free = 0.3824 target = 0.165401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.141283 restraints weight = 4325.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.142323 restraints weight = 3833.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.142682 restraints weight = 3494.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.143006 restraints weight = 3338.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.143100 restraints weight = 3257.851| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3791 Z= 0.111 Angle : 0.532 9.108 5152 Z= 0.282 Chirality : 0.044 0.146 558 Planarity : 0.004 0.039 663 Dihedral : 3.836 15.824 518 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.98 % Allowed : 17.33 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.76 (0.41), residues: 465 helix: -2.59 (0.96), residues: 29 sheet: -0.57 (0.42), residues: 154 loop : -0.11 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 325 TYR 0.014 0.001 TYR A 486 PHE 0.014 0.001 PHE A 540 TRP 0.010 0.002 TRP A 433 HIS 0.001 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 3784) covalent geometry : angle 0.53090 / 0.28 ( 5137) SS BOND : bond 0.00216 / 0.12 ( 6) SS BOND : angle 0.81081 / 0.41 ( 12) hydrogen bonds : bond 0.02771 / 1.97 ( 106) hydrogen bonds : angle 5.59512 / 3.76 ( 252) link_NAG-ASN : bond 0.00089 / 0.05 ( 1) link_NAG-ASN : angle 1.21388 / 0.70 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 929.83 seconds wall clock time: 16 minutes 43.33 seconds (1003.33 seconds total)