Starting phenix.real_space_refine on Wed Feb 4 07:45:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hhe_52170/02_2026/9hhe_52170.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hhe_52170/02_2026/9hhe_52170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hhe_52170/02_2026/9hhe_52170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hhe_52170/02_2026/9hhe_52170.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hhe_52170/02_2026/9hhe_52170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hhe_52170/02_2026/9hhe_52170.map" } resolution = 2.84 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 6170 2.51 5 N 1428 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9248 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4624 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 537} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4624 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 537} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.39, per 1000 atoms: 0.26 Number of scatterers: 9248 At special positions: 0 Unit cell: (76.818, 130.2, 103.509, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1616 8.00 N 1428 7.00 C 6170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.83 Conformation dependent library (CDL) restraints added in 316.5 milliseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 2 sheets defined 73.7% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 24 through 33 removed outlier: 3.695A pdb=" N ASN B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.640A pdb=" N LEU B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 148 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 155 through 176 Processing helix chain 'B' and resid 176 through 189 removed outlier: 3.861A pdb=" N PHE B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 217 Processing helix chain 'B' and resid 218 through 245 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 257 through 278 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 278 through 287 removed outlier: 3.586A pdb=" N ASN B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 320 removed outlier: 4.099A pdb=" N VAL B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Proline residue: B 313 - end of helix Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.755A pdb=" N THR B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA B 330 " --> pdb=" O HIS B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 330' Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'B' and resid 369 through 394 removed outlier: 3.995A pdb=" N VAL B 382 " --> pdb=" O MET B 378 " (cutoff:3.500A) Proline residue: B 383 - end of helix Processing helix chain 'B' and resid 402 through 411 Processing helix chain 'B' and resid 413 through 429 Processing helix chain 'B' and resid 430 through 433 Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 460 through 483 Processing helix chain 'B' and resid 509 through 534 Processing helix chain 'B' and resid 552 through 556 removed outlier: 3.502A pdb=" N ALA B 556 " --> pdb=" O TRP B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 591 Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.632A pdb=" N ARG A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 71 Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.576A pdb=" N LEU A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 147 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 155 through 176 Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.714A pdb=" N TYR A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 Processing helix chain 'A' and resid 218 through 245 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 278 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 278 through 287 removed outlier: 3.584A pdb=" N ASN A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 320 removed outlier: 4.098A pdb=" N VAL A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 369 through 394 removed outlier: 3.992A pdb=" N VAL A 382 " --> pdb=" O MET A 378 " (cutoff:3.500A) Proline residue: A 383 - end of helix Processing helix chain 'A' and resid 401 through 411 Processing helix chain 'A' and resid 413 through 429 Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 460 through 483 Processing helix chain 'A' and resid 509 through 534 Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 562 through 591 removed outlier: 3.551A pdb=" N SER A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 42 removed outlier: 3.550A pdb=" N SER B 75 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN B 17 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE B 73 " --> pdb=" O ASN B 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 42 removed outlier: 3.512A pdb=" N CYS A 12 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 75 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASN A 17 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE A 73 " --> pdb=" O ASN A 17 " (cutoff:3.500A) 614 hydrogen bonds defined for protein. 1824 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: 1.43 Time building geometry restraints manager: 1.07 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: 2673 1.34 - 1.45: 1575 1.45 - 1.57: 5218 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 9518 Sorted by residual: bond pdb=" N ASN B 28 " pdb=" CA ASN B 28 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.44e+00 bond pdb=" N LEU B 27 " pdb=" CA LEU B 27 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.23e-02 6.61e+03 5.73e+00 bond pdb=" CA LEU B 27 " pdb=" C LEU B 27 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.29e-02 6.01e+03 1.44e+00 bond pdb=" C ASN B 28 " pdb=" O ASN B 28 " ideal model delta sigma weight residual 1.237 1.249 -0.013 1.17e-02 7.31e+03 1.17e+00 bond pdb=" CB PHE B 180 " pdb=" CG PHE B 180 " ideal model delta sigma weight residual 1.502 1.526 -0.024 2.30e-02 1.89e+03 1.05e+00 ... (remaining 9513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 12762 2.05 - 4.10: 135 4.10 - 6.14: 32 6.14 - 8.19: 3 8.19 - 10.24: 4 Bond angle restraints: 12936 Sorted by residual: angle pdb=" CA GLN A 57 " pdb=" CB GLN A 57 " pdb=" CG GLN A 57 " ideal model delta sigma weight residual 114.10 120.39 -6.29 2.00e+00 2.50e-01 9.89e+00 angle pdb=" CA LEU A 197 " pdb=" CB LEU A 197 " pdb=" CG LEU A 197 " ideal model delta sigma weight residual 116.30 126.54 -10.24 3.50e+00 8.16e-02 8.56e+00 angle pdb=" CA LEU B 197 " pdb=" CB LEU B 197 " pdb=" CG LEU B 197 " ideal model delta sigma weight residual 116.30 126.32 -10.02 3.50e+00 8.16e-02 8.20e+00 angle pdb=" C ASN A 149 " pdb=" CA ASN A 149 " pdb=" CB ASN A 149 " ideal model delta sigma weight residual 110.42 115.92 -5.50 1.99e+00 2.53e-01 7.63e+00 angle pdb=" CA LEU B 70 " pdb=" CB LEU B 70 " pdb=" CG LEU B 70 " ideal model delta sigma weight residual 116.30 125.91 -9.61 3.50e+00 8.16e-02 7.54e+00 ... (remaining 12931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 4712 15.39 - 30.79: 631 30.79 - 46.18: 178 46.18 - 61.58: 57 61.58 - 76.97: 14 Dihedral angle restraints: 5592 sinusoidal: 2204 harmonic: 3388 Sorted by residual: dihedral pdb=" CA MET A 532 " pdb=" C MET A 532 " pdb=" N TYR A 533 " pdb=" CA TYR A 533 " ideal model delta harmonic sigma weight residual 180.00 -162.37 -17.63 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA MET B 532 " pdb=" C MET B 532 " pdb=" N TYR B 533 " pdb=" CA TYR B 533 " ideal model delta harmonic sigma weight residual -180.00 -162.66 -17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ARG B 478 " pdb=" CB ARG B 478 " pdb=" CG ARG B 478 " pdb=" CD ARG B 478 " ideal model delta sinusoidal sigma weight residual -60.00 -118.97 58.97 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 839 0.027 - 0.055: 347 0.055 - 0.082: 176 0.082 - 0.110: 86 0.110 - 0.137: 20 Chirality restraints: 1468 Sorted by residual: chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ASP B 71 " pdb=" N ASP B 71 " pdb=" C ASP B 71 " pdb=" CB ASP B 71 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1465 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 180 " -0.013 2.00e-02 2.50e+03 1.54e-02 4.17e+00 pdb=" CG PHE A 180 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 180 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 180 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 180 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 180 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 180 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 66 " 0.009 2.00e-02 2.50e+03 1.18e-02 2.44e+00 pdb=" CG PHE B 66 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE B 66 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 66 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 66 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 66 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 66 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 400 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.06e+00 pdb=" C PHE A 400 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE A 400 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL A 401 " 0.008 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 5094 3.00 - 3.47: 9989 3.47 - 3.95: 15589 3.95 - 4.42: 18084 4.42 - 4.90: 28777 Nonbonded interactions: 77533 Sorted by model distance: nonbonded pdb=" N GLN A 57 " pdb=" OE1 GLN A 57 " model vdw 2.521 3.120 nonbonded pdb=" OG1 THR A 170 " pdb=" OG SER A 519 " model vdw 2.569 3.040 nonbonded pdb=" OG1 THR B 170 " pdb=" OG SER B 519 " model vdw 2.569 3.040 nonbonded pdb=" O PHE A 400 " pdb=" N LYS A 402 " model vdw 2.595 3.120 nonbonded pdb=" O LYS A 32 " pdb=" NZ LYS A 32 " model vdw 2.613 3.120 ... (remaining 77528 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 8.350 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: 0.280 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.140 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:7.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 0.004 0.034 9518 Z= 0.164 Angle : 0.569 10.240 12936 Z= 0.292 Chirality : 0.042 0.137 1468 Planarity : 0.004 0.030 1578 Dihedral : 16.225 76.970 3384 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.86 % Favored : 95.96 % Rotamer: Outliers : 1.72 % Allowed : 21.93 % Favored : 76.34 % 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 are not related in a simple way. whole: 2.41 (0.26), residues: 1114 helix: 2.40 (0.18), residues: 768 sheet: 0.37 (0.85), residues: 52 loop : -0.35 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 54 TYR 0.023 0.001 TYR A 106 PHE 0.036 0.001 PHE A 180 TRP 0.016 0.001 TRP B 181 HIS 0.001 0.000 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9518) covalent geometry : angle 0.56910 (12936) hydrogen bonds : bond 0.12088 ( 614) hydrogen bonds : angle 5.61841 ( 1824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6978 (mm-30) REVERT: B 379 GLU cc_start: 0.7720 (pt0) cc_final: 0.7340 (pt0) REVERT: B 402 LYS cc_start: 0.7046 (tptt) cc_final: 0.6739 (tppt) REVERT: A 101 GLU cc_start: 0.7505 (mt-10) cc_final: 0.6974 (mm-30) REVERT: A 334 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8280 (m) REVERT: A 379 GLU cc_start: 0.7721 (pt0) cc_final: 0.7360 (pt0) outliers start: 18 outliers final: 12 residues processed: 91 average time/residue: 0.3875 time to fit residues: 39.1911 Evaluate side-chains 95 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN A 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.089833 restraints weight = 12073.926| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.20 r_work: 0.2861 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9518 Z= 0.133 Angle : 0.518 9.522 12936 Z= 0.264 Chirality : 0.042 0.153 1468 Planarity : 0.004 0.032 1578 Dihedral : 5.299 53.906 1214 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.95 % Favored : 95.87 % Rotamer: Outliers : 2.39 % Allowed : 21.17 % Favored : 76.44 % 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 are not related in a simple way. whole: 2.73 (0.27), residues: 1114 helix: 2.55 (0.18), residues: 776 sheet: 0.58 (0.85), residues: 52 loop : -0.04 (0.43), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.018 0.001 TYR B 106 PHE 0.022 0.001 PHE A 180 TRP 0.013 0.001 TRP B 181 HIS 0.001 0.000 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9518) covalent geometry : angle 0.51784 (12936) hydrogen bonds : bond 0.04546 ( 614) hydrogen bonds : angle 4.74874 ( 1824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6904 (mm-30) REVERT: B 379 GLU cc_start: 0.7713 (pt0) cc_final: 0.7327 (pt0) REVERT: B 402 LYS cc_start: 0.7177 (tptt) cc_final: 0.6815 (tppt) REVERT: B 478 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7835 (mtm180) REVERT: B 551 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7788 (tppt) REVERT: A 101 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6909 (mm-30) REVERT: A 379 GLU cc_start: 0.7718 (pt0) cc_final: 0.7346 (pt0) REVERT: A 418 LYS cc_start: 0.8416 (tptt) cc_final: 0.8100 (tppt) outliers start: 25 outliers final: 10 residues processed: 103 average time/residue: 0.3987 time to fit residues: 45.1190 Evaluate side-chains 92 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 328 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN B 110 ASN A 17 ASN A 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.091829 restraints weight = 12396.979| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.10 r_work: 0.2920 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9518 Z= 0.218 Angle : 0.553 9.253 12936 Z= 0.285 Chirality : 0.044 0.153 1468 Planarity : 0.004 0.037 1578 Dihedral : 5.082 53.750 1204 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.86 % Favored : 95.96 % Rotamer: Outliers : 3.16 % Allowed : 21.17 % Favored : 75.67 % 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 are not related in a simple way. whole: 2.51 (0.26), residues: 1114 helix: 2.41 (0.18), residues: 774 sheet: 0.27 (0.82), residues: 52 loop : -0.14 (0.42), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 33 TYR 0.016 0.002 TYR A 274 PHE 0.018 0.002 PHE A 66 TRP 0.017 0.002 TRP B 181 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 9518) covalent geometry : angle 0.55251 (12936) hydrogen bonds : bond 0.04818 ( 614) hydrogen bonds : angle 4.75949 ( 1824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6954 (mm-30) REVERT: B 379 GLU cc_start: 0.7731 (pt0) cc_final: 0.7349 (pt0) REVERT: B 551 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7801 (tppt) REVERT: A 101 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6954 (mm-30) REVERT: A 379 GLU cc_start: 0.7749 (pt0) cc_final: 0.7384 (pt0) outliers start: 33 outliers final: 17 residues processed: 104 average time/residue: 0.3792 time to fit residues: 43.3829 Evaluate side-chains 100 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN A 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.094413 restraints weight = 12414.318| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.06 r_work: 0.2950 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9518 Z= 0.138 Angle : 0.514 8.753 12936 Z= 0.262 Chirality : 0.042 0.150 1468 Planarity : 0.004 0.035 1578 Dihedral : 5.073 55.887 1204 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.13 % Favored : 95.69 % Rotamer: Outliers : 3.35 % Allowed : 21.55 % Favored : 75.10 % 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 are not related in a simple way. whole: 2.69 (0.27), residues: 1114 helix: 2.53 (0.19), residues: 776 sheet: 0.19 (0.81), residues: 52 loop : 0.01 (0.43), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.018 0.001 TYR B 106 PHE 0.024 0.001 PHE B 180 TRP 0.013 0.001 TRP B 181 HIS 0.001 0.000 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9518) covalent geometry : angle 0.51398 (12936) hydrogen bonds : bond 0.04357 ( 614) hydrogen bonds : angle 4.60522 ( 1824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.393 Fit side-chains REVERT: B 101 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6954 (mm-30) REVERT: B 379 GLU cc_start: 0.7709 (pt0) cc_final: 0.7332 (pt0) REVERT: B 402 LYS cc_start: 0.7260 (tptt) cc_final: 0.6870 (tppt) REVERT: B 478 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7542 (ttt-90) REVERT: B 551 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7807 (tppt) REVERT: A 101 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6954 (mm-30) REVERT: A 334 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8313 (m) REVERT: A 379 GLU cc_start: 0.7717 (pt0) cc_final: 0.7344 (pt0) REVERT: A 418 LYS cc_start: 0.8406 (tptt) cc_final: 0.8097 (tppt) REVERT: A 551 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7767 (tppt) outliers start: 35 outliers final: 10 residues processed: 110 average time/residue: 0.4028 time to fit residues: 48.7962 Evaluate side-chains 95 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN B 17 ASN B 110 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 ASN A 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.094549 restraints weight = 12309.474| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.04 r_work: 0.2951 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9518 Z= 0.151 Angle : 0.530 9.279 12936 Z= 0.269 Chirality : 0.042 0.187 1468 Planarity : 0.004 0.035 1578 Dihedral : 4.120 47.717 1200 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.13 % Favored : 95.69 % Rotamer: Outliers : 3.26 % Allowed : 22.03 % Favored : 74.71 % 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 are not related in a simple way. whole: 2.66 (0.27), residues: 1114 helix: 2.51 (0.18), residues: 778 sheet: 0.13 (0.80), residues: 52 loop : -0.03 (0.43), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 33 TYR 0.017 0.001 TYR A 274 PHE 0.014 0.001 PHE A 31 TRP 0.014 0.001 TRP B 181 HIS 0.001 0.000 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9518) covalent geometry : angle 0.52958 (12936) hydrogen bonds : bond 0.04370 ( 614) hydrogen bonds : angle 4.59222 ( 1824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 ASN cc_start: 0.8488 (m110) cc_final: 0.8278 (t0) REVERT: B 101 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6981 (mm-30) REVERT: B 379 GLU cc_start: 0.7710 (pt0) cc_final: 0.7329 (pt0) REVERT: A 101 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7012 (mm-30) REVERT: A 334 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8298 (m) REVERT: A 379 GLU cc_start: 0.7720 (pt0) cc_final: 0.7345 (pt0) REVERT: A 418 LYS cc_start: 0.8400 (tptt) cc_final: 0.8128 (tppt) REVERT: A 551 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7774 (tppt) outliers start: 34 outliers final: 13 residues processed: 111 average time/residue: 0.3964 time to fit residues: 48.4957 Evaluate side-chains 101 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 417 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 0.0020 chunk 87 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN A 17 ASN A 105 GLN A 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.140486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089816 restraints weight = 12110.768| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.20 r_work: 0.2863 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9518 Z= 0.131 Angle : 0.528 8.751 12936 Z= 0.267 Chirality : 0.042 0.149 1468 Planarity : 0.004 0.034 1578 Dihedral : 4.080 47.006 1200 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.77 % Favored : 96.05 % Rotamer: Outliers : 2.59 % Allowed : 22.70 % Favored : 74.71 % 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 are not related in a simple way. whole: 2.73 (0.27), residues: 1114 helix: 2.56 (0.18), residues: 778 sheet: 0.04 (0.80), residues: 52 loop : 0.03 (0.43), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 33 TYR 0.023 0.001 TYR B 106 PHE 0.026 0.001 PHE A 180 TRP 0.012 0.001 TRP B 181 HIS 0.001 0.000 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9518) covalent geometry : angle 0.52841 (12936) hydrogen bonds : bond 0.04202 ( 614) hydrogen bonds : angle 4.52556 ( 1824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7013 (mm-30) REVERT: B 379 GLU cc_start: 0.7713 (pt0) cc_final: 0.7324 (pt0) REVERT: B 402 LYS cc_start: 0.7114 (tptt) cc_final: 0.6713 (tppt) REVERT: B 551 LYS cc_start: 0.8766 (tppt) cc_final: 0.8312 (mmpt) REVERT: A 101 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7029 (mm-30) REVERT: A 379 GLU cc_start: 0.7695 (pt0) cc_final: 0.7317 (pt0) REVERT: A 418 LYS cc_start: 0.8406 (tptt) cc_final: 0.8147 (tppt) REVERT: A 551 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7766 (tppt) outliers start: 27 outliers final: 14 residues processed: 108 average time/residue: 0.4741 time to fit residues: 55.7693 Evaluate side-chains 103 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 98 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 0.0670 chunk 40 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN B 110 ASN A 57 GLN A 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.140808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.090127 restraints weight = 12201.133| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.21 r_work: 0.2871 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9518 Z= 0.127 Angle : 0.533 8.700 12936 Z= 0.268 Chirality : 0.041 0.148 1468 Planarity : 0.004 0.038 1578 Dihedral : 4.037 46.084 1200 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.13 % Favored : 95.78 % Rotamer: Outliers : 2.97 % Allowed : 22.41 % Favored : 74.62 % 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 are not related in a simple way. whole: 2.76 (0.27), residues: 1114 helix: 2.59 (0.19), residues: 778 sheet: 0.02 (0.79), residues: 52 loop : 0.01 (0.43), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 33 TYR 0.017 0.001 TYR A 274 PHE 0.026 0.001 PHE A 66 TRP 0.011 0.001 TRP B 181 HIS 0.001 0.000 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9518) covalent geometry : angle 0.53306 (12936) hydrogen bonds : bond 0.04126 ( 614) hydrogen bonds : angle 4.47374 ( 1824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: B 101 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7014 (mm-30) REVERT: B 276 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8581 (ttmt) REVERT: B 379 GLU cc_start: 0.7693 (pt0) cc_final: 0.7302 (pt0) REVERT: B 402 LYS cc_start: 0.7207 (tptt) cc_final: 0.6869 (tppt) REVERT: B 478 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7600 (ttt-90) REVERT: B 551 LYS cc_start: 0.8700 (tppt) cc_final: 0.8253 (mmpt) REVERT: A 46 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8907 (mt) REVERT: A 101 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7033 (mm-30) REVERT: A 334 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8309 (m) REVERT: A 379 GLU cc_start: 0.7697 (pt0) cc_final: 0.7315 (pt0) REVERT: A 418 LYS cc_start: 0.8391 (tptt) cc_final: 0.8131 (tppt) REVERT: A 551 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7753 (tppt) outliers start: 31 outliers final: 12 residues processed: 111 average time/residue: 0.4739 time to fit residues: 57.2753 Evaluate side-chains 102 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 94 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN A 110 ASN A 391 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.089062 restraints weight = 12094.263| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.19 r_work: 0.2853 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9518 Z= 0.159 Angle : 0.555 8.928 12936 Z= 0.281 Chirality : 0.043 0.148 1468 Planarity : 0.004 0.035 1578 Dihedral : 3.870 19.530 1198 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.13 % Favored : 95.78 % Rotamer: Outliers : 2.78 % Allowed : 23.18 % Favored : 74.04 % 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 are not related in a simple way. whole: 2.68 (0.27), residues: 1114 helix: 2.53 (0.18), residues: 778 sheet: -0.01 (0.80), residues: 52 loop : 0.01 (0.43), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 33 TYR 0.024 0.001 TYR B 106 PHE 0.028 0.001 PHE B 66 TRP 0.013 0.001 TRP B 181 HIS 0.001 0.000 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9518) covalent geometry : angle 0.55506 (12936) hydrogen bonds : bond 0.04302 ( 614) hydrogen bonds : angle 4.51123 ( 1824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: B 101 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7038 (mm-30) REVERT: B 276 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8573 (ttmt) REVERT: B 379 GLU cc_start: 0.7690 (pt0) cc_final: 0.7304 (pt0) REVERT: B 551 LYS cc_start: 0.8635 (tppt) cc_final: 0.8176 (mmpt) REVERT: A 46 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8913 (mt) REVERT: A 101 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7036 (mm-30) REVERT: A 276 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8557 (ttmt) REVERT: A 334 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8309 (m) REVERT: A 379 GLU cc_start: 0.7715 (pt0) cc_final: 0.7334 (pt0) REVERT: A 418 LYS cc_start: 0.8383 (tptt) cc_final: 0.8120 (tppt) REVERT: A 551 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7760 (tppt) outliers start: 29 outliers final: 14 residues processed: 106 average time/residue: 0.4777 time to fit residues: 55.1785 Evaluate side-chains 103 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.089728 restraints weight = 12135.620| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.20 r_work: 0.2860 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9518 Z= 0.138 Angle : 0.552 10.453 12936 Z= 0.277 Chirality : 0.042 0.147 1468 Planarity : 0.004 0.033 1578 Dihedral : 3.843 18.706 1198 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 2.30 % Allowed : 23.95 % Favored : 73.75 % 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 are not related in a simple way. whole: 2.71 (0.27), residues: 1114 helix: 2.57 (0.19), residues: 778 sheet: -0.01 (0.80), residues: 52 loop : -0.03 (0.43), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 33 TYR 0.024 0.001 TYR B 106 PHE 0.033 0.001 PHE A 180 TRP 0.011 0.001 TRP B 181 HIS 0.001 0.000 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9518) covalent geometry : angle 0.55232 (12936) hydrogen bonds : bond 0.04171 ( 614) hydrogen bonds : angle 4.46115 ( 1824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7017 (mm-30) REVERT: B 276 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8566 (ttmt) REVERT: B 379 GLU cc_start: 0.7677 (pt0) cc_final: 0.7280 (pt0) REVERT: B 402 LYS cc_start: 0.7099 (tptt) cc_final: 0.6759 (tppt) REVERT: B 551 LYS cc_start: 0.8558 (tppt) cc_final: 0.8126 (mmpt) REVERT: A 46 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8949 (mt) REVERT: A 101 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7010 (mm-30) REVERT: A 276 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8556 (ttmt) REVERT: A 334 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8305 (m) REVERT: A 379 GLU cc_start: 0.7682 (pt0) cc_final: 0.7296 (pt0) REVERT: A 418 LYS cc_start: 0.8377 (tptt) cc_final: 0.8111 (tppt) outliers start: 24 outliers final: 12 residues processed: 101 average time/residue: 0.4039 time to fit residues: 44.4729 Evaluate side-chains 102 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 4 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN A 17 ASN A 110 ASN A 391 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.140344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.090369 restraints weight = 12082.906| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.20 r_work: 0.2872 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9518 Z= 0.128 Angle : 0.547 9.483 12936 Z= 0.276 Chirality : 0.042 0.146 1468 Planarity : 0.004 0.033 1578 Dihedral : 3.816 18.420 1198 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Rotamer: Outliers : 2.20 % Allowed : 23.95 % Favored : 73.85 % 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 are not related in a simple way. whole: 2.75 (0.27), residues: 1114 helix: 2.59 (0.19), residues: 778 sheet: 0.02 (0.80), residues: 52 loop : -0.00 (0.43), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 33 TYR 0.023 0.001 TYR B 106 PHE 0.033 0.001 PHE A 180 TRP 0.010 0.001 TRP B 181 HIS 0.001 0.000 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9518) covalent geometry : angle 0.54721 (12936) hydrogen bonds : bond 0.04091 ( 614) hydrogen bonds : angle 4.41304 ( 1824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: B 28 ASN cc_start: 0.8547 (m110) cc_final: 0.8345 (p0) REVERT: B 74 GLU cc_start: 0.8613 (tt0) cc_final: 0.8239 (tp30) REVERT: B 101 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7014 (mm-30) REVERT: B 276 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8575 (ttmt) REVERT: B 379 GLU cc_start: 0.7666 (pt0) cc_final: 0.7275 (pt0) REVERT: B 551 LYS cc_start: 0.8518 (tppt) cc_final: 0.8116 (mmpt) REVERT: A 46 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8968 (mt) REVERT: A 101 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7007 (mm-30) REVERT: A 276 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8565 (ttmt) REVERT: A 334 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8296 (m) REVERT: A 379 GLU cc_start: 0.7687 (pt0) cc_final: 0.7305 (pt0) REVERT: A 418 LYS cc_start: 0.8380 (tptt) cc_final: 0.8113 (tppt) outliers start: 23 outliers final: 11 residues processed: 101 average time/residue: 0.4111 time to fit residues: 45.3677 Evaluate side-chains 99 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.0470 chunk 88 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.140592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.090530 restraints weight = 12041.673| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.20 r_work: 0.2876 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9518 Z= 0.127 Angle : 0.551 9.469 12936 Z= 0.277 Chirality : 0.042 0.147 1468 Planarity : 0.004 0.033 1578 Dihedral : 3.798 18.288 1198 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 2.01 % Allowed : 24.23 % Favored : 73.75 % 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 are not related in a simple way. whole: 2.78 (0.27), residues: 1114 helix: 2.61 (0.19), residues: 778 sheet: -0.00 (0.79), residues: 52 loop : 0.01 (0.43), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 33 TYR 0.024 0.001 TYR A 106 PHE 0.012 0.001 PHE B 66 TRP 0.010 0.001 TRP A 181 HIS 0.001 0.000 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9518) covalent geometry : angle 0.55107 (12936) hydrogen bonds : bond 0.04063 ( 614) hydrogen bonds : angle 4.38776 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3143.03 seconds wall clock time: 54 minutes 33.33 seconds (3273.33 seconds total)