Starting phenix.real_space_refine on Sat May 10 02:37:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3m_61119/05_2025/9j3m_61119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3m_61119/05_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_61119/05_2025/9j3m_61119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3m_61119/05_2025/9j3m_61119.map" model { file = "/net/cci-nas-00/data/ceres_data/9j3m_61119/05_2025/9j3m_61119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3m_61119/05_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-5687/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: 3.36, per 1000 atoms: 0.71 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: 1.26 Conformation dependent library (CDL) restraints added in 587.1 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: 0.53 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: 1.35 Time building geometry restraints manager: 1.46 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: 0.830 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.220 ------------------------------------------------------------------------------- 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 : 0.540 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: 0.8812 time to fit residues: 99.2357 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 : 0.495 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134513 restraints weight = 5114.660| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.69 r_work: 0.3367 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 2.04655 ( 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 : 0.507 Fit side-chains REVERT: A 122 MET cc_start: 0.9030 (ttp) cc_final: 0.8652 (ttp) REVERT: A 172 THR cc_start: 0.8107 (m) cc_final: 0.7897 (m) REVERT: A 176 ASN cc_start: 0.8125 (m110) cc_final: 0.7893 (m110) REVERT: A 356 MET cc_start: 0.5080 (mmt) cc_final: 0.4808 (mmp) REVERT: A 444 VAL cc_start: 0.8317 (p) cc_final: 0.7826 (m) outliers start: 8 outliers final: 4 residues processed: 102 average time/residue: 0.8693 time to fit residues: 93.5726 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 : 0.507 ------------------------------------------------------------------------------- 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: 0.2980 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 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 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 = 0.3977 r_free = 0.3977 target = 0.166746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133623 restraints weight = 5134.599| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.67 r_work: 0.3377 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1733 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= 0.160 Angle : 0.632 6.981 6563 Z= 0.322 Chirality : 0.042 0.136 747 Planarity : 0.005 0.060 795 Dihedral : 7.579 109.192 656 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.19 % Allowed : 11.75 % 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: -0.05 (0.34), residues: 595 helix: 0.65 (0.26), residues: 383 sheet: -1.41 (0.66), residues: 46 loop : -1.03 (0.50), residues: 166 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 0.016 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 0.04741 ( 331) hydrogen bonds : angle 5.01889 ( 969) SS BOND : bond 0.00368 ( 1) SS BOND : angle 2.05221 ( 2) covalent geometry : bond 0.00362 ( 4824) covalent geometry : angle 0.63082 ( 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 109 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.472 Fit side-chains REVERT: A 122 MET cc_start: 0.9041 (ttp) cc_final: 0.8660 (ttp) REVERT: A 176 ASN cc_start: 0.8162 (m110) cc_final: 0.7863 (m-40) REVERT: A 356 MET cc_start: 0.5076 (mmt) cc_final: 0.4805 (mmp) REVERT: A 444 VAL cc_start: 0.8276 (p) cc_final: 0.7813 (m) REVERT: B 46 GLU cc_start: 0.8548 (tt0) cc_final: 0.8240 (pt0) outliers start: 11 outliers final: 8 residues processed: 100 average time/residue: 0.7599 time to fit residues: 80.4566 Evaluate side-chains 101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.0040 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.163281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129338 restraints weight = 5151.484| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.72 r_work: 0.3455 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4825 Z= 0.140 Angle : 0.604 6.583 6563 Z= 0.307 Chirality : 0.041 0.140 747 Planarity : 0.005 0.058 795 Dihedral : 7.260 103.433 656 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.39 % Allowed : 11.55 % Favored : 85.06 % 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: 0.38 (0.35), residues: 595 helix: 0.97 (0.27), residues: 386 sheet: -1.31 (0.68), residues: 46 loop : -0.82 (0.51), 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 257 TYR 0.015 0.001 TYR A 378 ARG 0.001 0.000 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 331) hydrogen bonds : angle 4.84492 ( 969) SS BOND : bond 0.00029 ( 1) SS BOND : angle 2.15875 ( 2) covalent geometry : bond 0.00312 ( 4824) covalent geometry : angle 0.60249 ( 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 115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.506 Fit side-chains REVERT: A 122 MET cc_start: 0.9064 (ttp) cc_final: 0.8705 (ttp) REVERT: A 176 ASN cc_start: 0.8083 (m110) cc_final: 0.7815 (m-40) REVERT: A 216 ASP cc_start: 0.8590 (m-30) cc_final: 0.8316 (m-30) REVERT: A 356 MET cc_start: 0.4860 (mmt) cc_final: 0.4646 (mmt) REVERT: A 444 VAL cc_start: 0.8296 (p) cc_final: 0.7826 (m) REVERT: B 46 GLU cc_start: 0.8570 (tt0) cc_final: 0.8336 (pt0) outliers start: 17 outliers final: 9 residues processed: 104 average time/residue: 0.7794 time to fit residues: 85.8146 Evaluate side-chains 101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 314 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 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 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 = 0.3913 r_free = 0.3913 target = 0.161456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126815 restraints weight = 5202.336| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.73 r_work: 0.3431 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2069 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 : 0.613 6.715 6563 Z= 0.313 Chirality : 0.042 0.139 747 Planarity : 0.005 0.057 795 Dihedral : 7.170 102.056 656 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.59 % Allowed : 12.35 % Favored : 84.06 % 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: 0.59 (0.35), residues: 595 helix: 1.10 (0.27), residues: 384 sheet: -1.22 (0.69), residues: 46 loop : -0.62 (0.52), residues: 165 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 0.012 0.002 PHE A 128 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 4.86419 ( 969) SS BOND : bond 0.00571 ( 1) SS BOND : angle 2.75067 ( 2) covalent geometry : bond 0.00396 ( 4824) covalent geometry : angle 0.61089 ( 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 121 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.535 Fit side-chains REVERT: A 122 MET cc_start: 0.9090 (ttp) cc_final: 0.8727 (ttp) REVERT: A 176 ASN cc_start: 0.8064 (m110) cc_final: 0.7792 (m-40) REVERT: A 216 ASP cc_start: 0.8591 (m-30) cc_final: 0.8338 (m-30) REVERT: A 356 MET cc_start: 0.4895 (mmt) cc_final: 0.4676 (mmt) REVERT: A 444 VAL cc_start: 0.8372 (p) cc_final: 0.7892 (m) REVERT: B 46 GLU cc_start: 0.8596 (tt0) cc_final: 0.8374 (pt0) outliers start: 18 outliers final: 12 residues processed: 108 average time/residue: 0.7659 time to fit residues: 87.6813 Evaluate side-chains 110 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP 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 A residue 568 LYS 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: 0.9980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 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 B 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.161352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126650 restraints weight = 5174.969| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.73 r_work: 0.3428 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4825 Z= 0.171 Angle : 0.608 6.681 6563 Z= 0.311 Chirality : 0.042 0.138 747 Planarity : 0.005 0.057 795 Dihedral : 7.082 98.815 656 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.78 % Allowed : 12.95 % 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: 0.74 (0.35), residues: 595 helix: 1.17 (0.27), residues: 387 sheet: -1.26 (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 B 110 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 A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 331) hydrogen bonds : angle 4.84068 ( 969) SS BOND : bond 0.00494 ( 1) SS BOND : angle 2.34726 ( 2) covalent geometry : bond 0.00392 ( 4824) covalent geometry : angle 0.60706 ( 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 125 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.479 Fit side-chains REVERT: A 122 MET cc_start: 0.9053 (ttp) cc_final: 0.8722 (ttp) REVERT: A 176 ASN cc_start: 0.8088 (m110) cc_final: 0.7804 (m-40) REVERT: A 216 ASP cc_start: 0.8615 (m-30) cc_final: 0.8368 (m-30) REVERT: A 311 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8447 (m) REVERT: A 356 MET cc_start: 0.5003 (mmt) cc_final: 0.4767 (mmt) REVERT: A 444 VAL cc_start: 0.8396 (p) cc_final: 0.7922 (m) REVERT: B 46 GLU cc_start: 0.8591 (tt0) cc_final: 0.8368 (pt0) outliers start: 19 outliers final: 10 residues processed: 113 average time/residue: 0.7229 time to fit residues: 86.6972 Evaluate side-chains 113 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 A residue 568 LYS 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: 0.3980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.161601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126867 restraints weight = 5092.197| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.72 r_work: 0.3432 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2215 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= 0.165 Angle : 0.610 6.661 6563 Z= 0.311 Chirality : 0.042 0.139 747 Planarity : 0.005 0.058 795 Dihedral : 6.979 94.794 656 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.39 % Allowed : 13.94 % Favored : 82.67 % 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: 0.85 (0.36), residues: 595 helix: 1.25 (0.27), residues: 387 sheet: -1.26 (0.66), residues: 46 loop : -0.38 (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 0.012 0.001 PHE A 128 TYR 0.015 0.001 TYR A 378 ARG 0.001 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 331) hydrogen bonds : angle 4.82201 ( 969) SS BOND : bond 0.00438 ( 1) SS BOND : angle 2.11325 ( 2) covalent geometry : bond 0.00379 ( 4824) covalent geometry : angle 0.60926 ( 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: 17 poor density : 103 time to evaluate : 0.569 Fit side-chains REVERT: A 122 MET cc_start: 0.9044 (ttp) cc_final: 0.8707 (ttp) REVERT: A 176 ASN cc_start: 0.8057 (m110) cc_final: 0.7796 (m-40) REVERT: A 216 ASP cc_start: 0.8647 (m-30) cc_final: 0.8378 (m-30) REVERT: A 311 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8439 (m) REVERT: A 356 MET cc_start: 0.4968 (mmt) cc_final: 0.4735 (mmt) REVERT: A 444 VAL cc_start: 0.8368 (p) cc_final: 0.7887 (m) REVERT: B 46 GLU cc_start: 0.8579 (tt0) cc_final: 0.8360 (pt0) outliers start: 17 outliers final: 11 residues processed: 108 average time/residue: 0.7677 time to fit residues: 87.8323 Evaluate side-chains 111 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 104 THR 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: 0.9980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.162952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128523 restraints weight = 5152.285| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.73 r_work: 0.3450 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2281 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= 0.144 Angle : 0.599 6.631 6563 Z= 0.303 Chirality : 0.042 0.140 747 Planarity : 0.005 0.060 795 Dihedral : 6.802 90.495 656 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.39 % Allowed : 14.14 % Favored : 82.47 % 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: 0.89 (0.36), residues: 595 helix: 1.35 (0.27), residues: 383 sheet: -1.26 (0.66), residues: 46 loop : -0.49 (0.54), residues: 166 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 0.012 0.001 PHE A 128 TYR 0.014 0.001 TYR A 378 ARG 0.001 0.000 ARG A 299 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 331) hydrogen bonds : angle 4.74122 ( 969) SS BOND : bond 0.00311 ( 1) SS BOND : angle 1.70816 ( 2) covalent geometry : bond 0.00323 ( 4824) covalent geometry : angle 0.59875 ( 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 121 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.566 Fit side-chains REVERT: A 122 MET cc_start: 0.9027 (ttm) cc_final: 0.8697 (ttp) REVERT: A 176 ASN cc_start: 0.8050 (m110) cc_final: 0.7813 (m-40) REVERT: A 216 ASP cc_start: 0.8570 (m-30) cc_final: 0.8317 (m-30) REVERT: A 221 THR cc_start: 0.8894 (p) cc_final: 0.8573 (t) REVERT: A 311 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8410 (m) REVERT: A 356 MET cc_start: 0.4858 (mmt) cc_final: 0.4643 (mmt) REVERT: A 444 VAL cc_start: 0.8339 (p) cc_final: 0.7870 (m) REVERT: B 46 GLU cc_start: 0.8543 (tt0) cc_final: 0.8332 (pt0) outliers start: 17 outliers final: 10 residues processed: 110 average time/residue: 0.7561 time to fit residues: 88.0964 Evaluate side-chains 112 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.163500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.129041 restraints weight = 5162.665| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.74 r_work: 0.3462 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2389 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= 0.142 Angle : 0.599 6.608 6563 Z= 0.302 Chirality : 0.042 0.139 747 Planarity : 0.005 0.056 795 Dihedral : 6.657 86.460 656 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.79 % Allowed : 15.14 % Favored : 82.07 % 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: 0.99 (0.36), residues: 595 helix: 1.42 (0.27), residues: 383 sheet: -1.14 (0.66), residues: 46 loop : -0.46 (0.54), residues: 166 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 0.04341 ( 331) hydrogen bonds : angle 4.71408 ( 969) SS BOND : bond 0.00337 ( 1) SS BOND : angle 1.72713 ( 2) covalent geometry : bond 0.00320 ( 4824) covalent geometry : angle 0.59878 ( 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: 14 poor density : 109 time to evaluate : 0.512 Fit side-chains REVERT: A 122 MET cc_start: 0.9042 (ttm) cc_final: 0.8723 (ttp) REVERT: A 176 ASN cc_start: 0.8026 (m110) cc_final: 0.7818 (m110) REVERT: A 216 ASP cc_start: 0.8586 (m-30) cc_final: 0.8320 (m-30) REVERT: A 221 THR cc_start: 0.8867 (p) cc_final: 0.8556 (t) REVERT: A 311 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8411 (m) REVERT: A 323 MET cc_start: 0.8983 (mmt) cc_final: 0.8599 (mmt) REVERT: A 356 MET cc_start: 0.4820 (mmt) cc_final: 0.4611 (mmt) REVERT: A 444 VAL cc_start: 0.8322 (p) cc_final: 0.7858 (m) outliers start: 14 outliers final: 9 residues processed: 112 average time/residue: 0.7481 time to fit residues: 88.9515 Evaluate side-chains 116 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 B 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.163948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129671 restraints weight = 5158.784| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.73 r_work: 0.3481 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4825 Z= 0.138 Angle : 0.599 6.590 6563 Z= 0.302 Chirality : 0.042 0.139 747 Planarity : 0.005 0.059 795 Dihedral : 6.522 82.267 656 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.59 % Allowed : 15.54 % 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: 1.07 (0.36), residues: 595 helix: 1.45 (0.27), residues: 386 sheet: -1.08 (0.66), residues: 46 loop : -0.40 (0.55), residues: 163 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 0.012 0.001 PHE A 128 TYR 0.013 0.001 TYR A 378 ARG 0.001 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 331) hydrogen bonds : angle 4.68281 ( 969) SS BOND : bond 0.00283 ( 1) SS BOND : angle 1.62034 ( 2) covalent geometry : bond 0.00309 ( 4824) covalent geometry : angle 0.59882 ( 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 122 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.512 Fit side-chains REVERT: A 122 MET cc_start: 0.9029 (ttm) cc_final: 0.8709 (ttp) REVERT: A 176 ASN cc_start: 0.7977 (m110) cc_final: 0.7758 (m110) REVERT: A 216 ASP cc_start: 0.8565 (m-30) cc_final: 0.8299 (m-30) REVERT: A 221 THR cc_start: 0.8799 (p) cc_final: 0.8504 (t) REVERT: A 311 VAL cc_start: 0.8653 (p) cc_final: 0.8421 (m) REVERT: A 316 MET cc_start: 0.8685 (mtp) cc_final: 0.8429 (mtm) REVERT: A 323 MET cc_start: 0.8963 (mmt) cc_final: 0.8572 (mmt) REVERT: A 402 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7955 (pt0) REVERT: A 444 VAL cc_start: 0.8292 (p) cc_final: 0.7841 (m) outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 0.7591 time to fit residues: 91.7765 Evaluate side-chains 117 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 84 SER 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: 0.5980 chunk 45 optimal weight: 0.0470 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.164313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130118 restraints weight = 5162.143| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.74 r_work: 0.3473 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4825 Z= 0.135 Angle : 0.610 6.876 6563 Z= 0.306 Chirality : 0.042 0.183 747 Planarity : 0.005 0.058 795 Dihedral : 6.447 78.941 656 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.39 % Allowed : 16.14 % Favored : 81.47 % 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: 1.17 (0.36), residues: 595 helix: 1.51 (0.27), residues: 386 sheet: -1.02 (0.67), residues: 46 loop : -0.32 (0.55), residues: 163 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 0.012 0.001 PHE A 128 TYR 0.013 0.001 TYR B 107 ARG 0.001 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 331) hydrogen bonds : angle 4.64931 ( 969) SS BOND : bond 0.00283 ( 1) SS BOND : angle 1.57399 ( 2) covalent geometry : bond 0.00299 ( 4824) covalent geometry : angle 0.60908 ( 6561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3597.96 seconds wall clock time: 62 minutes 44.77 seconds (3764.77 seconds total)