Starting phenix.real_space_refine on Wed Sep 17 05:02:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3m_61119/09_2025/9j3m_61119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3m_61119/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j3m_61119/09_2025/9j3m_61119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3m_61119/09_2025/9j3m_61119.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j3m_61119/09_2025/9j3m_61119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3m_61119/09_2025/9j3m_61119.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.091 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.27, per 1000 atoms: 0.27 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: 0.40 Conformation dependent library (CDL) restraints added in 205.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.15 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: 0.72 Time building geometry restraints manager: 0.55 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: 1.130 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.400 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 58 TYR 0.013 0.001 TYR A 378 PHE 0.022 0.002 PHE A 123 TRP 0.026 0.002 TRP A 389 HIS 0.001 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 4824) covalent geometry : angle 0.75575 ( 6561) SS BOND : bond 0.00268 ( 1) SS BOND : angle 2.52707 ( 2) hydrogen bonds : bond 0.21203 ( 331) hydrogen bonds : angle 8.12069 ( 969) *********************** 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 : 0.178 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: 0.4366 time to fit residues: 49.0182 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 : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.0040 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.166792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133387 restraints weight = 5214.625| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.71 r_work: 0.3359 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4825 Z= 0.168 Angle : 0.676 7.834 6563 Z= 0.346 Chirality : 0.043 0.140 747 Planarity : 0.006 0.071 795 Dihedral : 8.226 124.911 656 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.59 % Allowed : 7.97 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.33), residues: 595 helix: -0.03 (0.25), residues: 391 sheet: -1.68 (0.63), residues: 48 loop : -1.32 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 58 TYR 0.014 0.001 TYR A 331 PHE 0.024 0.002 PHE A 123 TRP 0.009 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 4824) covalent geometry : angle 0.67504 ( 6561) SS BOND : bond 0.00573 ( 1) SS BOND : angle 2.17858 ( 2) hydrogen bonds : bond 0.05254 ( 331) hydrogen bonds : angle 5.39418 ( 969) *********************** 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 : 0.183 Fit side-chains REVERT: A 122 MET cc_start: 0.9069 (ttp) cc_final: 0.8699 (ttp) REVERT: A 356 MET cc_start: 0.5064 (mmt) cc_final: 0.4809 (mmp) outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.3973 time to fit residues: 42.8897 Evaluate side-chains 95 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 314 LYS 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: 0.6980 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.166290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132970 restraints weight = 5140.097| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.69 r_work: 0.3371 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1725 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= 0.168 Angle : 0.639 6.976 6563 Z= 0.327 Chirality : 0.042 0.136 747 Planarity : 0.005 0.060 795 Dihedral : 7.623 108.950 656 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.79 % Allowed : 12.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.34), residues: 595 helix: 0.56 (0.26), residues: 385 sheet: -1.42 (0.66), residues: 46 loop : -0.99 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 234 TYR 0.016 0.001 TYR A 378 PHE 0.016 0.002 PHE A 295 TRP 0.009 0.001 TRP A 309 HIS 0.000 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4824) covalent geometry : angle 0.63824 ( 6561) SS BOND : bond 0.00332 ( 1) SS BOND : angle 2.12033 ( 2) hydrogen bonds : bond 0.04799 ( 331) hydrogen bonds : angle 5.06084 ( 969) *********************** 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 110 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.187 Fit side-chains REVERT: A 122 MET cc_start: 0.9042 (ttp) cc_final: 0.8662 (ttp) REVERT: A 167 PHE cc_start: 0.8178 (t80) cc_final: 0.7971 (t80) REVERT: A 216 ASP cc_start: 0.8780 (m-30) cc_final: 0.8575 (m-30) REVERT: A 356 MET cc_start: 0.5091 (mmt) cc_final: 0.4818 (mmp) REVERT: B 46 GLU cc_start: 0.8568 (tt0) cc_final: 0.8255 (pt0) outliers start: 14 outliers final: 8 residues processed: 100 average time/residue: 0.3996 time to fit residues: 42.1772 Evaluate side-chains 98 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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 104 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 0.0040 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.3750 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.163975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130152 restraints weight = 5160.886| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.73 r_work: 0.3462 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4825 Z= 0.133 Angle : 0.600 6.610 6563 Z= 0.305 Chirality : 0.041 0.141 747 Planarity : 0.005 0.058 795 Dihedral : 7.234 102.631 656 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.39 % Allowed : 13.15 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.35), residues: 595 helix: 0.99 (0.27), residues: 386 sheet: -1.31 (0.68), residues: 46 loop : -0.81 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 58 TYR 0.015 0.001 TYR A 378 PHE 0.014 0.002 PHE A 295 TRP 0.007 0.001 TRP A 309 HIS 0.000 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4824) covalent geometry : angle 0.59891 ( 6561) SS BOND : bond 0.00375 ( 1) SS BOND : angle 2.08158 ( 2) hydrogen bonds : bond 0.04333 ( 331) hydrogen bonds : angle 4.81434 ( 969) *********************** 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 109 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.176 Fit side-chains REVERT: A 122 MET cc_start: 0.9047 (ttp) cc_final: 0.8684 (ttp) REVERT: A 356 MET cc_start: 0.4856 (mmt) cc_final: 0.4645 (mmt) REVERT: B 46 GLU cc_start: 0.8567 (tt0) cc_final: 0.8342 (pt0) outliers start: 12 outliers final: 6 residues processed: 101 average time/residue: 0.3637 time to fit residues: 38.9182 Evaluate side-chains 97 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 404 SER Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.161232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126363 restraints weight = 5169.395| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.74 r_work: 0.3426 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2049 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= 0.177 Angle : 0.618 6.705 6563 Z= 0.316 Chirality : 0.042 0.138 747 Planarity : 0.005 0.057 795 Dihedral : 7.177 101.841 656 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.39 % Allowed : 14.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.35), residues: 595 helix: 1.07 (0.27), residues: 384 sheet: -1.23 (0.69), residues: 46 loop : -0.63 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 134 TYR 0.015 0.001 TYR A 378 PHE 0.013 0.002 PHE A 295 TRP 0.007 0.001 TRP A 309 HIS 0.000 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 4824) covalent geometry : angle 0.61553 ( 6561) SS BOND : bond 0.00651 ( 1) SS BOND : angle 2.96638 ( 2) hydrogen bonds : bond 0.04627 ( 331) hydrogen bonds : angle 4.88395 ( 969) *********************** 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 112 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.182 Fit side-chains REVERT: A 122 MET cc_start: 0.9090 (ttp) cc_final: 0.8732 (ttp) REVERT: A 356 MET cc_start: 0.5015 (mmt) cc_final: 0.4778 (mmt) REVERT: B 46 GLU cc_start: 0.8563 (tt0) cc_final: 0.8336 (pt0) outliers start: 12 outliers final: 6 residues processed: 104 average time/residue: 0.3843 time to fit residues: 42.2049 Evaluate side-chains 106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 404 SER Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.161084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126113 restraints weight = 5198.621| |-----------------------------------------------------------------------------| 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: 3.73 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2094 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= 0.181 Angle : 0.619 6.712 6563 Z= 0.316 Chirality : 0.043 0.138 747 Planarity : 0.005 0.057 795 Dihedral : 7.121 98.894 656 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.19 % Allowed : 14.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.35), residues: 595 helix: 1.11 (0.27), residues: 387 sheet: -1.20 (0.69), residues: 46 loop : -0.47 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 134 TYR 0.016 0.001 TYR A 378 PHE 0.018 0.002 PHE A 295 TRP 0.007 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 4824) covalent geometry : angle 0.61768 ( 6561) SS BOND : bond 0.00505 ( 1) SS BOND : angle 2.38635 ( 2) hydrogen bonds : bond 0.04662 ( 331) hydrogen bonds : angle 4.89029 ( 969) *********************** 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 122 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.110 Fit side-chains REVERT: A 122 MET cc_start: 0.9089 (ttp) cc_final: 0.8722 (ttp) REVERT: A 356 MET cc_start: 0.5042 (mmt) cc_final: 0.4802 (mmt) REVERT: B 46 GLU cc_start: 0.8563 (tt0) cc_final: 0.8330 (pt0) outliers start: 16 outliers final: 10 residues processed: 112 average time/residue: 0.3523 time to fit residues: 41.7833 Evaluate side-chains 113 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.0060 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.163469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128897 restraints weight = 5152.610| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.73 r_work: 0.3455 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2272 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= 0.139 Angle : 0.595 6.627 6563 Z= 0.302 Chirality : 0.042 0.139 747 Planarity : 0.005 0.058 795 Dihedral : 6.881 92.381 656 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.79 % Allowed : 14.94 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.36), residues: 595 helix: 1.31 (0.27), residues: 385 sheet: -1.21 (0.68), residues: 46 loop : -0.46 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 58 TYR 0.014 0.001 TYR A 378 PHE 0.012 0.001 PHE A 128 TRP 0.007 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4824) covalent geometry : angle 0.59451 ( 6561) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.70178 ( 2) hydrogen bonds : bond 0.04362 ( 331) hydrogen bonds : angle 4.75846 ( 969) *********************** 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 115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.179 Fit side-chains REVERT: A 122 MET cc_start: 0.9037 (ttp) cc_final: 0.8706 (ttp) REVERT: A 323 MET cc_start: 0.8961 (mmt) cc_final: 0.8546 (mmt) REVERT: A 356 MET cc_start: 0.4862 (mmt) cc_final: 0.4642 (mmt) REVERT: B 13 GLN cc_start: 0.8913 (mm110) cc_final: 0.8512 (mm-40) REVERT: B 46 GLU cc_start: 0.8547 (tt0) cc_final: 0.8333 (pt0) REVERT: B 119 SER cc_start: 0.9180 (m) cc_final: 0.8863 (p) outliers start: 14 outliers final: 8 residues processed: 105 average time/residue: 0.3817 time to fit residues: 42.3197 Evaluate side-chains 108 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 549 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.162754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128065 restraints weight = 5202.486| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.75 r_work: 0.3442 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4825 Z= 0.151 Angle : 0.601 6.635 6563 Z= 0.305 Chirality : 0.042 0.138 747 Planarity : 0.005 0.059 795 Dihedral : 6.783 90.292 656 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.99 % Allowed : 14.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.36), residues: 595 helix: 1.34 (0.27), residues: 386 sheet: -1.21 (0.67), residues: 46 loop : -0.43 (0.56), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 58 TYR 0.014 0.001 TYR A 378 PHE 0.012 0.001 PHE A 128 TRP 0.007 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 4824) covalent geometry : angle 0.60070 ( 6561) SS BOND : bond 0.00373 ( 1) SS BOND : angle 1.86759 ( 2) hydrogen bonds : bond 0.04399 ( 331) hydrogen bonds : angle 4.75599 ( 969) *********************** 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 116 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.193 Fit side-chains REVERT: A 122 MET cc_start: 0.9041 (ttp) cc_final: 0.8722 (ttp) REVERT: A 323 MET cc_start: 0.8979 (mmt) cc_final: 0.8569 (mmt) REVERT: A 356 MET cc_start: 0.4873 (mmt) cc_final: 0.4655 (mmt) REVERT: B 46 GLU cc_start: 0.8540 (tt0) cc_final: 0.8329 (pt0) outliers start: 15 outliers final: 9 residues processed: 107 average time/residue: 0.4003 time to fit residues: 45.2310 Evaluate side-chains 108 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.162202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127531 restraints weight = 5072.987| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.72 r_work: 0.3441 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2334 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 : 0.612 6.662 6563 Z= 0.310 Chirality : 0.042 0.138 747 Planarity : 0.005 0.056 795 Dihedral : 6.760 87.883 656 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.59 % Allowed : 15.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.36), residues: 595 helix: 1.29 (0.27), residues: 388 sheet: -1.17 (0.67), residues: 46 loop : -0.39 (0.55), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 58 TYR 0.015 0.001 TYR A 378 PHE 0.012 0.001 PHE A 128 TRP 0.007 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4824) covalent geometry : angle 0.61077 ( 6561) SS BOND : bond 0.00404 ( 1) SS BOND : angle 1.95828 ( 2) hydrogen bonds : bond 0.04524 ( 331) hydrogen bonds : angle 4.79647 ( 969) *********************** 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 111 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.128 Fit side-chains REVERT: A 122 MET cc_start: 0.9036 (ttp) cc_final: 0.8706 (ttp) REVERT: A 311 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8454 (m) REVERT: A 316 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: A 356 MET cc_start: 0.4879 (mmt) cc_final: 0.4657 (mmt) REVERT: B 46 GLU cc_start: 0.8544 (tt0) cc_final: 0.8341 (pt0) outliers start: 13 outliers final: 10 residues processed: 102 average time/residue: 0.4029 time to fit residues: 43.3092 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 : 0.222 ------------------------------------------------------------------------------- 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 316 MET 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 44 optimal weight: 0.0000 chunk 34 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.164213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129644 restraints weight = 5153.372| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.76 r_work: 0.3488 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2440 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= 0.137 Angle : 0.596 6.596 6563 Z= 0.300 Chirality : 0.041 0.139 747 Planarity : 0.005 0.059 795 Dihedral : 6.575 81.922 656 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.99 % Allowed : 14.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.36), residues: 595 helix: 1.42 (0.27), residues: 386 sheet: -1.11 (0.66), residues: 46 loop : -0.42 (0.55), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 58 TYR 0.013 0.001 TYR A 378 PHE 0.012 0.001 PHE A 128 TRP 0.007 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4824) covalent geometry : angle 0.59548 ( 6561) SS BOND : bond 0.00239 ( 1) SS BOND : angle 1.50669 ( 2) hydrogen bonds : bond 0.04281 ( 331) hydrogen bonds : angle 4.68415 ( 969) ********************** 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 115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.156 Fit side-chains REVERT: A 122 MET cc_start: 0.9037 (ttp) cc_final: 0.8765 (ttp) REVERT: A 311 VAL cc_start: 0.8638 (p) cc_final: 0.8400 (m) REVERT: A 323 MET cc_start: 0.8959 (mmt) cc_final: 0.8547 (mmt) REVERT: A 402 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8048 (pt0) outliers start: 15 outliers final: 10 residues processed: 106 average time/residue: 0.3879 time to fit residues: 43.3252 Evaluate side-chains 114 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.162995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128248 restraints weight = 5155.105| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.75 r_work: 0.3441 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4825 Z= 0.159 Angle : 0.627 6.960 6563 Z= 0.316 Chirality : 0.043 0.201 747 Planarity : 0.005 0.058 795 Dihedral : 6.585 81.600 656 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.99 % Allowed : 16.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.36), residues: 595 helix: 1.38 (0.27), residues: 386 sheet: -1.04 (0.67), residues: 46 loop : -0.43 (0.55), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 58 TYR 0.015 0.001 TYR A 378 PHE 0.012 0.001 PHE A 128 TRP 0.007 0.001 TRP B 110 HIS 0.000 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4824) covalent geometry : angle 0.62651 ( 6561) SS BOND : bond 0.00407 ( 1) SS BOND : angle 1.85258 ( 2) hydrogen bonds : bond 0.04450 ( 331) hydrogen bonds : angle 4.73110 ( 969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1797.88 seconds wall clock time: 31 minutes 24.67 seconds (1884.67 seconds total)