Starting phenix.real_space_refine on Sun Apr 27 05:49:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3m_61119/04_2025/9j3m_61119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3m_61119/04_2025/9j3m_61119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j3m_61119/04_2025/9j3m_61119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3m_61119/04_2025/9j3m_61119.map" model { file = "/net/cci-nas-00/data/ceres_data/9j3m_61119/04_2025/9j3m_61119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3m_61119/04_2025/9j3m_61119.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.091 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 28 5.16 5 C 3098 2.51 5 N 739 2.21 5 O 832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4700 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3719 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 25, 'TRANS': 453} Chain: "B" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 949 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.67, per 1000 atoms: 0.78 Number of scatterers: 4700 At special positions: 0 Unit cell: (72.54, 74.4, 109.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 3 15.00 O 832 8.00 N 739 7.00 C 3098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 586.5 milliseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 3 sheets defined 71.6% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 143 removed outlier: 3.550A pdb=" N LYS A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Proline residue: A 118 - end of helix removed outlier: 3.906A pdb=" N ASP A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 removed outlier: 4.196A pdb=" N PHE A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 176 removed outlier: 3.898A pdb=" N ASN A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 201 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.565A pdb=" N ILE A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 removed outlier: 3.788A pdb=" N GLY A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 266 through 273 Processing helix chain 'A' and resid 273 through 297 removed outlier: 3.607A pdb=" N LEU A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 338 removed outlier: 3.548A pdb=" N VAL A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 365 removed outlier: 4.097A pdb=" N LYS A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 397 removed outlier: 3.590A pdb=" N THR A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLY A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 433 removed outlier: 4.072A pdb=" N GLN A 426 " --> pdb=" O MET A 422 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASN A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 457 removed outlier: 4.006A pdb=" N THR A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 462 through 469 removed outlier: 4.132A pdb=" N VAL A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.888A pdb=" N ASP A 497 " --> pdb=" O TYR A 493 " (cutoff:3.500A) Proline residue: A 498 - end of helix Processing helix chain 'A' and resid 510 through 522 removed outlier: 3.749A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 518 " --> pdb=" O LYS A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 543 Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 548 through 575 removed outlier: 3.629A pdb=" N GLY A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A 554 " --> pdb=" O PRO A 550 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12 removed outlier: 4.179A pdb=" N TYR B 33 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 336 hydrogen bonds defined for protein. 969 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: 1.51 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1378 1.34 - 1.46: 1031 1.46 - 1.58: 2366 1.58 - 1.69: 1 1.69 - 1.81: 48 Bond restraints: 4824 Sorted by residual: bond pdb=" C4 ADP A 701 " pdb=" C5 ADP A 701 " ideal model delta sigma weight residual 1.490 1.423 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O2A ADP A 701 " pdb=" PA ADP A 701 " ideal model delta sigma weight residual 1.510 1.446 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O1A ADP A 701 " pdb=" PA ADP A 701 " ideal model delta sigma weight residual 1.510 1.452 0.058 2.00e-02 2.50e+03 8.40e+00 bond pdb=" C2' ADP A 701 " pdb=" C3' ADP A 701 " ideal model delta sigma weight residual 1.524 1.472 0.052 2.00e-02 2.50e+03 6.87e+00 bond pdb=" C5 ADP A 701 " pdb=" C6 ADP A 701 " ideal model delta sigma weight residual 1.490 1.439 0.051 2.00e-02 2.50e+03 6.55e+00 ... (remaining 4819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 6357 1.83 - 3.65: 154 3.65 - 5.48: 36 5.48 - 7.31: 11 7.31 - 9.13: 3 Bond angle restraints: 6561 Sorted by residual: angle pdb=" C ILE A 151 " pdb=" N ILE A 152 " pdb=" CA ILE A 152 " ideal model delta sigma weight residual 120.24 123.75 -3.51 6.30e-01 2.52e+00 3.10e+01 angle pdb=" N VAL B 63 " pdb=" CA VAL B 63 " pdb=" C VAL B 63 " ideal model delta sigma weight residual 113.47 110.00 3.47 1.01e+00 9.80e-01 1.18e+01 angle pdb=" C LEU A 577 " pdb=" N ARG A 578 " pdb=" CA ARG A 578 " ideal model delta sigma weight residual 121.80 127.50 -5.70 1.71e+00 3.42e-01 1.11e+01 angle pdb=" C ARG A 299 " pdb=" N LYS A 300 " pdb=" CA LYS A 300 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C THR A 420 " pdb=" N MET A 421 " pdb=" CA MET A 421 " ideal model delta sigma weight residual 121.66 116.26 5.40 1.76e+00 3.23e-01 9.42e+00 ... (remaining 6556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.43: 2723 27.43 - 54.87: 83 54.87 - 82.30: 6 82.30 - 109.74: 0 109.74 - 137.17: 1 Dihedral angle restraints: 2813 sinusoidal: 1079 harmonic: 1734 Sorted by residual: dihedral pdb=" O1B ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PB ADP A 701 " pdb=" PA ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 77.17 -137.17 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" CA LYS A 516 " pdb=" C LYS A 516 " pdb=" N ALA A 517 " pdb=" CA ALA A 517 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" C5' ADP A 701 " pdb=" O5' ADP A 701 " pdb=" PA ADP A 701 " pdb=" O2A ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -140.80 80.81 1 2.00e+01 2.50e-03 2.02e+01 ... (remaining 2810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 544 0.041 - 0.082: 164 0.082 - 0.123: 34 0.123 - 0.165: 3 0.165 - 0.206: 2 Chirality restraints: 747 Sorted by residual: chirality pdb=" CG LEU A 577 " pdb=" CB LEU A 577 " pdb=" CD1 LEU A 577 " pdb=" CD2 LEU A 577 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CG LEU B 18 " pdb=" CB LEU B 18 " pdb=" CD1 LEU B 18 " pdb=" CD2 LEU B 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA THR A 549 " pdb=" N THR A 549 " pdb=" C THR A 549 " pdb=" CB THR A 549 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 744 not shown) Planarity restraints: 795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 350 " -0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO A 351 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 351 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 351 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 379 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C GLY A 379 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY A 379 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE A 380 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 463 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO A 464 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " -0.032 5.00e-02 4.00e+02 ... (remaining 792 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 299 2.74 - 3.28: 4891 3.28 - 3.82: 8214 3.82 - 4.36: 10335 4.36 - 4.90: 16926 Nonbonded interactions: 40665 Sorted by model distance: nonbonded pdb=" O VAL A 292 " pdb=" OG SER A 296 " model vdw 2.196 3.040 nonbonded pdb=" O VAL A 139 " pdb=" OG1 THR A 143 " model vdw 2.204 3.040 nonbonded pdb=" O ARG A 369 " pdb=" OG1 THR A 373 " model vdw 2.223 3.040 nonbonded pdb=" O TYR B 52 " pdb=" NH1 ARG B 71 " model vdw 2.229 3.120 nonbonded pdb=" O PRO A 525 " pdb=" OG SER A 529 " model vdw 2.245 3.040 ... (remaining 40660 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.005 0.067 4825 Z= 0.222 Angle : 0.757 9.134 6563 Z= 0.392 Chirality : 0.041 0.206 747 Planarity : 0.006 0.082 795 Dihedral : 12.771 137.173 1706 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.30), residues: 595 helix: -1.43 (0.23), residues: 385 sheet: -2.28 (0.59), residues: 48 loop : -1.63 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 389 HIS 0.001 0.000 HIS A 210 PHE 0.022 0.002 PHE A 123 TYR 0.013 0.001 TYR A 378 ARG 0.003 0.000 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.21203 ( 331) hydrogen bonds : angle 8.12069 ( 969) SS BOND : bond 0.00268 ( 1) SS BOND : angle 2.52707 ( 2) covalent geometry : bond 0.00451 ( 4824) covalent geometry : angle 0.75575 ( 6561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.513 Fit side-chains REVERT: A 172 THR cc_start: 0.8168 (m) cc_final: 0.7952 (m) REVERT: A 176 ASN cc_start: 0.8149 (m110) cc_final: 0.7949 (m110) REVERT: A 276 LEU cc_start: 0.8578 (mt) cc_final: 0.8323 (mt) REVERT: A 356 MET cc_start: 0.5184 (mmt) cc_final: 0.4848 (mmp) REVERT: A 431 LYS cc_start: 0.7808 (tttp) cc_final: 0.7608 (ttmm) REVERT: A 471 MET cc_start: 0.8697 (mtm) cc_final: 0.8344 (mtm) REVERT: A 483 LEU cc_start: 0.8318 (mt) cc_final: 0.8098 (mm) REVERT: A 554 MET cc_start: 0.8728 (mtt) cc_final: 0.8459 (mtt) REVERT: B 58 ARG cc_start: 0.8507 (mtm110) cc_final: 0.8278 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.9256 time to fit residues: 104.2772 Evaluate side-chains 97 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.0040 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 335 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.167631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134513 restraints weight = 5114.656| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.69 r_work: 0.3361 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4825 Z= 0.157 Angle : 0.672 7.681 6563 Z= 0.344 Chirality : 0.043 0.138 747 Planarity : 0.006 0.070 795 Dihedral : 8.180 123.396 656 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.59 % Allowed : 8.17 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.33), residues: 595 helix: 0.04 (0.25), residues: 391 sheet: -1.66 (0.63), residues: 48 loop : -1.30 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 PHE 0.026 0.002 PHE A 123 TYR 0.015 0.001 TYR A 331 ARG 0.002 0.000 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 331) hydrogen bonds : angle 5.32841 ( 969) SS BOND : bond 0.00504 ( 1) SS BOND : angle 2.04654 ( 2) covalent geometry : bond 0.00342 ( 4824) covalent geometry : angle 0.67155 ( 6561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.446 Fit side-chains REVERT: A 122 MET cc_start: 0.9082 (ttp) cc_final: 0.8726 (ttp) REVERT: A 172 THR cc_start: 0.8209 (m) cc_final: 0.8006 (m) REVERT: A 176 ASN cc_start: 0.8106 (m110) cc_final: 0.7905 (m110) REVERT: A 356 MET cc_start: 0.5056 (mmt) cc_final: 0.4800 (mmp) REVERT: A 444 VAL cc_start: 0.8512 (p) cc_final: 0.8027 (m) outliers start: 8 outliers final: 4 residues processed: 102 average time/residue: 0.8674 time to fit residues: 93.2298 Evaluate side-chains 97 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 297 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.165992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132572 restraints weight = 5122.925| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.68 r_work: 0.3361 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4825 Z= 0.176 Angle : 0.640 6.994 6563 Z= 0.327 Chirality : 0.042 0.137 747 Planarity : 0.005 0.060 795 Dihedral : 7.622 109.611 656 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.99 % Allowed : 10.96 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.34), residues: 595 helix: 0.58 (0.26), residues: 386 sheet: -1.42 (0.66), residues: 46 loop : -0.95 (0.50), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 309 HIS 0.000 0.000 HIS A 210 PHE 0.017 0.002 PHE A 295 TYR 0.016 0.001 TYR A 378 ARG 0.002 0.000 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 331) hydrogen bonds : angle 5.07453 ( 969) SS BOND : bond 0.00409 ( 1) SS BOND : angle 2.19699 ( 2) covalent geometry : bond 0.00401 ( 4824) covalent geometry : angle 0.63891 ( 6561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.473 Fit side-chains REVERT: A 122 MET cc_start: 0.9039 (ttp) cc_final: 0.8658 (ttp) REVERT: A 176 ASN cc_start: 0.8167 (m110) cc_final: 0.7884 (m-40) REVERT: A 356 MET cc_start: 0.5086 (mmt) cc_final: 0.4815 (mmp) REVERT: A 444 VAL cc_start: 0.8326 (p) cc_final: 0.7847 (m) REVERT: B 46 GLU cc_start: 0.8564 (tt0) cc_final: 0.8254 (pt0) outliers start: 15 outliers final: 10 residues processed: 104 average time/residue: 0.7396 time to fit residues: 81.6232 Evaluate side-chains 102 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 104 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.161657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127505 restraints weight = 5145.491| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.72 r_work: 0.3436 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4825 Z= 0.157 Angle : 0.615 6.664 6563 Z= 0.314 Chirality : 0.042 0.142 747 Planarity : 0.005 0.058 795 Dihedral : 7.349 104.684 656 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.99 % Allowed : 12.15 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.35), residues: 595 helix: 0.94 (0.27), residues: 384 sheet: -1.30 (0.68), residues: 46 loop : -0.85 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 309 HIS 0.000 0.000 HIS A 210 PHE 0.016 0.002 PHE A 295 TYR 0.015 0.001 TYR A 378 ARG 0.001 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 331) hydrogen bonds : angle 4.92832 ( 969) SS BOND : bond 0.00224 ( 1) SS BOND : angle 2.62016 ( 2) covalent geometry : bond 0.00352 ( 4824) covalent geometry : angle 0.61318 ( 6561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.478 Fit side-chains REVERT: A 122 MET cc_start: 0.9079 (ttp) cc_final: 0.8711 (ttp) REVERT: A 176 ASN cc_start: 0.8088 (m110) cc_final: 0.7819 (m-40) REVERT: A 216 ASP cc_start: 0.8609 (m-30) cc_final: 0.8348 (m-30) REVERT: A 356 MET cc_start: 0.4975 (mmt) cc_final: 0.4748 (mmt) REVERT: A 444 VAL cc_start: 0.8383 (p) cc_final: 0.7902 (m) REVERT: A 551 TYR cc_start: 0.8288 (m-80) cc_final: 0.8082 (m-80) REVERT: B 46 GLU cc_start: 0.8604 (tt0) cc_final: 0.8362 (pt0) outliers start: 15 outliers final: 9 residues processed: 104 average time/residue: 0.7826 time to fit residues: 86.2150 Evaluate side-chains 106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 84 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.161062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126407 restraints weight = 5209.517| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.73 r_work: 0.3423 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4825 Z= 0.170 Angle : 0.614 6.699 6563 Z= 0.315 Chirality : 0.042 0.141 747 Planarity : 0.005 0.056 795 Dihedral : 7.195 101.648 656 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.19 % Allowed : 12.55 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.35), residues: 595 helix: 1.03 (0.27), residues: 386 sheet: -1.20 (0.69), residues: 46 loop : -0.55 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 309 HIS 0.000 0.000 HIS A 210 PHE 0.012 0.002 PHE A 128 TYR 0.016 0.001 TYR A 378 ARG 0.001 0.000 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 331) hydrogen bonds : angle 4.88781 ( 969) SS BOND : bond 0.00624 ( 1) SS BOND : angle 2.91559 ( 2) covalent geometry : bond 0.00389 ( 4824) covalent geometry : angle 0.61231 ( 6561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.502 Fit side-chains REVERT: A 122 MET cc_start: 0.9083 (ttp) cc_final: 0.8713 (ttp) REVERT: A 176 ASN cc_start: 0.8065 (m110) cc_final: 0.7773 (m-40) REVERT: A 216 ASP cc_start: 0.8615 (m-30) cc_final: 0.8372 (m-30) REVERT: A 356 MET cc_start: 0.4989 (mmt) cc_final: 0.4761 (mmt) REVERT: A 444 VAL cc_start: 0.8379 (p) cc_final: 0.7899 (m) REVERT: B 46 GLU cc_start: 0.8588 (tt0) cc_final: 0.8366 (pt0) outliers start: 16 outliers final: 10 residues processed: 111 average time/residue: 0.7435 time to fit residues: 87.5279 Evaluate side-chains 115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127194 restraints weight = 5174.040| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.73 r_work: 0.3439 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4825 Z= 0.156 Angle : 0.601 6.688 6563 Z= 0.307 Chirality : 0.042 0.141 747 Planarity : 0.005 0.057 795 Dihedral : 7.018 96.869 656 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.19 % Allowed : 13.94 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.35), residues: 595 helix: 1.19 (0.27), residues: 387 sheet: -1.19 (0.68), residues: 46 loop : -0.44 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 309 HIS 0.000 0.000 HIS A 210 PHE 0.014 0.001 PHE A 295 TYR 0.015 0.001 TYR A 378 ARG 0.001 0.000 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.04480 ( 331) hydrogen bonds : angle 4.81299 ( 969) SS BOND : bond 0.00402 ( 1) SS BOND : angle 2.07796 ( 2) covalent geometry : bond 0.00354 ( 4824) covalent geometry : angle 0.60043 ( 6561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.471 Fit side-chains REVERT: A 122 MET cc_start: 0.9040 (ttp) cc_final: 0.8704 (ttp) REVERT: A 176 ASN cc_start: 0.8089 (m110) cc_final: 0.7820 (m-40) REVERT: A 216 ASP cc_start: 0.8614 (m-30) cc_final: 0.8363 (m-30) REVERT: A 356 MET cc_start: 0.5010 (mmt) cc_final: 0.4775 (mmt) REVERT: A 444 VAL cc_start: 0.8381 (p) cc_final: 0.7908 (m) REVERT: B 46 GLU cc_start: 0.8584 (tt0) cc_final: 0.8365 (pt0) outliers start: 16 outliers final: 9 residues processed: 105 average time/residue: 0.7852 time to fit residues: 87.2567 Evaluate side-chains 107 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.161148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.126303 restraints weight = 5098.256| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.73 r_work: 0.3426 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4825 Z= 0.172 Angle : 0.616 6.716 6563 Z= 0.314 Chirality : 0.042 0.143 747 Planarity : 0.005 0.055 795 Dihedral : 6.946 93.543 656 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.19 % Allowed : 13.55 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.36), residues: 595 helix: 1.21 (0.27), residues: 387 sheet: -1.26 (0.67), residues: 46 loop : -0.35 (0.55), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 PHE 0.015 0.002 PHE A 295 TYR 0.016 0.001 TYR A 378 ARG 0.002 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 331) hydrogen bonds : angle 4.84489 ( 969) SS BOND : bond 0.00475 ( 1) SS BOND : angle 2.22383 ( 2) covalent geometry : bond 0.00396 ( 4824) covalent geometry : angle 0.61482 ( 6561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.505 Fit side-chains REVERT: A 122 MET cc_start: 0.9036 (ttm) cc_final: 0.8705 (ttp) REVERT: A 176 ASN cc_start: 0.8101 (m110) cc_final: 0.7821 (m-40) REVERT: A 216 ASP cc_start: 0.8624 (m-30) cc_final: 0.8370 (m-30) REVERT: A 311 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8452 (m) REVERT: A 323 MET cc_start: 0.8977 (mmt) cc_final: 0.8584 (mmt) REVERT: A 356 MET cc_start: 0.5034 (mmt) cc_final: 0.4801 (mmt) REVERT: A 444 VAL cc_start: 0.8386 (p) cc_final: 0.7904 (m) REVERT: B 46 GLU cc_start: 0.8573 (tt0) cc_final: 0.8355 (pt0) outliers start: 16 outliers final: 10 residues processed: 108 average time/residue: 0.7534 time to fit residues: 86.3169 Evaluate side-chains 114 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 48 optimal weight: 0.0070 chunk 54 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.166998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133452 restraints weight = 5198.162| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.74 r_work: 0.3512 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4825 Z= 0.118 Angle : 0.581 6.496 6563 Z= 0.291 Chirality : 0.041 0.144 747 Planarity : 0.005 0.058 795 Dihedral : 6.541 82.580 656 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.79 % Allowed : 13.75 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.36), residues: 595 helix: 1.46 (0.27), residues: 389 sheet: -1.06 (0.67), residues: 46 loop : -0.43 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 PHE 0.013 0.001 PHE A 128 TYR 0.013 0.001 TYR B 107 ARG 0.001 0.000 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 331) hydrogen bonds : angle 4.56371 ( 969) SS BOND : bond 0.00104 ( 1) SS BOND : angle 1.23568 ( 2) covalent geometry : bond 0.00250 ( 4824) covalent geometry : angle 0.58080 ( 6561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.501 Fit side-chains REVERT: A 122 MET cc_start: 0.9021 (ttm) cc_final: 0.8795 (ttp) REVERT: A 216 ASP cc_start: 0.8573 (m-30) cc_final: 0.8297 (m-30) REVERT: A 311 VAL cc_start: 0.8635 (p) cc_final: 0.8418 (m) REVERT: A 316 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8421 (mtm) REVERT: A 323 MET cc_start: 0.8904 (mmt) cc_final: 0.8544 (mmt) REVERT: A 402 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7943 (pt0) REVERT: A 444 VAL cc_start: 0.8106 (p) cc_final: 0.7677 (m) outliers start: 14 outliers final: 9 residues processed: 110 average time/residue: 0.8832 time to fit residues: 102.7315 Evaluate side-chains 108 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 1 optimal weight: 0.0270 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.164597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130475 restraints weight = 5192.663| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.74 r_work: 0.3476 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4825 Z= 0.141 Angle : 0.610 6.521 6563 Z= 0.307 Chirality : 0.043 0.199 747 Planarity : 0.005 0.057 795 Dihedral : 6.479 81.862 656 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.99 % Allowed : 15.34 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.36), residues: 595 helix: 1.49 (0.27), residues: 387 sheet: -1.01 (0.67), residues: 46 loop : -0.44 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 PHE 0.012 0.001 PHE A 128 TYR 0.013 0.001 TYR A 378 ARG 0.001 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 331) hydrogen bonds : angle 4.61920 ( 969) SS BOND : bond 0.00314 ( 1) SS BOND : angle 1.75416 ( 2) covalent geometry : bond 0.00317 ( 4824) covalent geometry : angle 0.60945 ( 6561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.537 Fit side-chains REVERT: A 122 MET cc_start: 0.9060 (ttm) cc_final: 0.8836 (ttp) REVERT: A 176 ASN cc_start: 0.8030 (m110) cc_final: 0.7794 (m110) REVERT: A 216 ASP cc_start: 0.8558 (m-30) cc_final: 0.8288 (m-30) REVERT: A 311 VAL cc_start: 0.8651 (p) cc_final: 0.8423 (m) REVERT: A 323 MET cc_start: 0.8937 (mmt) cc_final: 0.8586 (mmt) REVERT: A 402 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7950 (pt0) REVERT: A 444 VAL cc_start: 0.8175 (p) cc_final: 0.7755 (m) outliers start: 15 outliers final: 9 residues processed: 112 average time/residue: 0.8772 time to fit residues: 104.7178 Evaluate side-chains 117 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 0.0030 chunk 40 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 24 optimal weight: 0.0970 chunk 30 optimal weight: 0.5980 chunk 52 optimal weight: 0.0470 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.2686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.166940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132844 restraints weight = 5162.577| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.77 r_work: 0.3521 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4825 Z= 0.122 Angle : 0.602 6.444 6563 Z= 0.301 Chirality : 0.043 0.194 747 Planarity : 0.005 0.059 795 Dihedral : 6.324 75.989 656 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.19 % Allowed : 15.94 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.36), residues: 595 helix: 1.60 (0.27), residues: 387 sheet: -1.00 (0.68), residues: 46 loop : -0.38 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 PHE 0.013 0.001 PHE A 128 TYR 0.014 0.001 TYR B 107 ARG 0.001 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 331) hydrogen bonds : angle 4.51362 ( 969) SS BOND : bond 0.00171 ( 1) SS BOND : angle 1.31962 ( 2) covalent geometry : bond 0.00261 ( 4824) covalent geometry : angle 0.60125 ( 6561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.519 Fit side-chains REVERT: A 122 MET cc_start: 0.9028 (ttm) cc_final: 0.8801 (ttp) REVERT: A 216 ASP cc_start: 0.8546 (m-30) cc_final: 0.8263 (m-30) REVERT: A 221 THR cc_start: 0.8839 (p) cc_final: 0.8508 (t) REVERT: A 287 PHE cc_start: 0.8849 (m-10) cc_final: 0.8644 (m-10) REVERT: A 311 VAL cc_start: 0.8633 (p) cc_final: 0.8415 (m) REVERT: A 323 MET cc_start: 0.8920 (mmt) cc_final: 0.8587 (mmt) REVERT: A 402 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7988 (pt0) REVERT: A 444 VAL cc_start: 0.8080 (p) cc_final: 0.7670 (m) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 0.8104 time to fit residues: 89.4030 Evaluate side-chains 103 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.162681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127535 restraints weight = 5130.203| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.76 r_work: 0.3443 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4825 Z= 0.171 Angle : 0.639 6.577 6563 Z= 0.323 Chirality : 0.045 0.189 747 Planarity : 0.005 0.058 795 Dihedral : 6.328 77.307 656 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.99 % Allowed : 16.73 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.36), residues: 595 helix: 1.52 (0.27), residues: 389 sheet: -0.99 (0.69), residues: 46 loop : -0.19 (0.56), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 PHE 0.012 0.002 PHE A 128 TYR 0.015 0.001 TYR A 378 ARG 0.001 0.000 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 331) hydrogen bonds : angle 4.68449 ( 969) SS BOND : bond 0.00440 ( 1) SS BOND : angle 1.99055 ( 2) covalent geometry : bond 0.00397 ( 4824) covalent geometry : angle 0.63831 ( 6561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3833.26 seconds wall clock time: 67 minutes 0.51 seconds (4020.51 seconds total)