Starting phenix.real_space_refine on Fri Jul 3 16:48:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pnt_17784/07_2026/8pnt_17784_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pnt_17784/07_2026/8pnt_17784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pnt_17784/07_2026/8pnt_17784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pnt_17784/07_2026/8pnt_17784.map" model { file = "/net/cci-nas-00/data/ceres_data/8pnt_17784/07_2026/8pnt_17784_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pnt_17784/07_2026/8pnt_17784_trim.cif" } resolution = 3.46 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= 0.001 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 44 5.16 5 C 4854 2.51 5 N 1305 2.21 5 O 1403 1.98 5 H 7508 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15117 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 12251 Classifications: {'peptide': 749} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 708} Chain breaks: 2 Chain: "B" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 2416 Classifications: {'peptide': 151} Link IDs: {'TRANS': 150} Chain: "C" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 306 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 111 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'MGT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.69, per 1000 atoms: 0.18 Number of scatterers: 15117 At special positions: 0 Unit cell: (99.002, 92.29, 114.943, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 3 15.00 O 1403 8.00 N 1305 7.00 C 4854 6.00 H 7508 1.00 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: 1.37 Conformation dependent library (CDL) restraints added in 475.0 milliseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 2 sheets defined 71.2% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.569A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 60 Processing helix chain 'A' and resid 64 through 79 Processing helix chain 'A' and resid 82 through 97 removed outlier: 3.523A pdb=" N VAL A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'A' and resid 120 through 136 removed outlier: 3.765A pdb=" N ASN A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 155 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 162 through 204 removed outlier: 3.652A pdb=" N ARG A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 6.636A pdb=" N LYS A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.502A pdb=" N LEU A 214 " --> pdb=" O HIS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 308 through 325 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 368 through 383 removed outlier: 4.148A pdb=" N TYR A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 401 Processing helix chain 'A' and resid 406 through 424 Processing helix chain 'A' and resid 429 through 438 removed outlier: 4.921A pdb=" N ASP A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 438 " --> pdb=" O ASP A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 470 through 477 removed outlier: 4.460A pdb=" N ALA A 475 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 removed outlier: 4.309A pdb=" N SER A 494 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 540 through 555 Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.539A pdb=" N PHE A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 577 Processing helix chain 'A' and resid 579 through 594 Processing helix chain 'A' and resid 597 through 611 Processing helix chain 'A' and resid 615 through 624 removed outlier: 3.719A pdb=" N PHE A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 634 through 675 removed outlier: 3.965A pdb=" N TRP A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 732 Processing helix chain 'A' and resid 737 through 754 Processing helix chain 'A' and resid 754 through 769 removed outlier: 4.961A pdb=" N GLN A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR A 761 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N THR A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 removed outlier: 3.963A pdb=" N VAL A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 782 " --> pdb=" O ILE A 778 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 28 through 37 Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.648A pdb=" N ILE B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 133 through 139 Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'C' and resid 116 through 132 Processing sheet with id=AA1, first strand: chain 'B' and resid 66 through 73 removed outlier: 5.229A pdb=" N PHE B 83 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 41 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 105 through 106 470 hydrogen bonds defined for protein. 1344 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: 3.28 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7486 1.03 - 1.23: 22 1.23 - 1.42: 3294 1.42 - 1.62: 4427 1.62 - 1.81: 66 Bond restraints: 15295 Sorted by residual: bond pdb=" O3B MGT B 201 " pdb=" PG MGT B 201 " ideal model delta sigma weight residual 1.729 1.614 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" O3A MGT B 201 " pdb=" PB MGT B 201 " ideal model delta sigma weight residual 1.676 1.600 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.28e+00 bond pdb=" O5' MGT B 201 " pdb=" PA MGT B 201 " ideal model delta sigma weight residual 1.657 1.602 0.055 2.00e-02 2.50e+03 7.69e+00 bond pdb=" N ARG B 112 " pdb=" H ARG B 112 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.52e+00 ... (remaining 15290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 27554 2.88 - 5.76: 71 5.76 - 8.64: 5 8.64 - 11.52: 1 11.52 - 14.40: 1 Bond angle restraints: 27632 Sorted by residual: angle pdb=" C5 MGT B 201 " pdb=" N7 MGT B 201 " pdb=" CM7 MGT B 201 " ideal model delta sigma weight residual 111.85 126.25 -14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" CA ILE B 111 " pdb=" C ILE B 111 " pdb=" O ILE B 111 " ideal model delta sigma weight residual 121.59 118.00 3.59 1.03e+00 9.43e-01 1.22e+01 angle pdb=" C8 MGT B 201 " pdb=" N7 MGT B 201 " pdb=" CM7 MGT B 201 " ideal model delta sigma weight residual 113.56 123.38 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA ILE B 110 " pdb=" C ILE B 110 " pdb=" O ILE B 110 " ideal model delta sigma weight residual 120.78 116.93 3.85 1.25e+00 6.40e-01 9.50e+00 angle pdb=" C THR B 113 " pdb=" N ASP B 114 " pdb=" CA ASP B 114 " ideal model delta sigma weight residual 122.21 126.95 -4.74 1.62e+00 3.81e-01 8.55e+00 ... (remaining 27627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6624 17.69 - 35.38: 403 35.38 - 53.07: 109 53.07 - 70.76: 31 70.76 - 88.45: 7 Dihedral angle restraints: 7174 sinusoidal: 3881 harmonic: 3293 Sorted by residual: dihedral pdb=" CA GLN A 245 " pdb=" C GLN A 245 " pdb=" N GLU A 246 " pdb=" CA GLU A 246 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA LYS A 37 " pdb=" C LYS A 37 " pdb=" N VAL A 38 " pdb=" CA VAL A 38 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CG ARG B 146 " pdb=" CD ARG B 146 " pdb=" NE ARG B 146 " pdb=" CZ ARG B 146 " ideal model delta sinusoidal sigma weight residual 180.00 136.27 43.73 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 7171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 995 0.050 - 0.100: 125 0.100 - 0.150: 26 0.150 - 0.200: 1 0.200 - 0.250: 2 Chirality restraints: 1149 Sorted by residual: chirality pdb=" C1' MGT B 201 " pdb=" C2' MGT B 201 " pdb=" N9 MGT B 201 " pdb=" O4' MGT B 201 " both_signs ideal model delta sigma weight residual False 2.21 2.46 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE B 110 " pdb=" N ILE B 110 " pdb=" C ILE B 110 " pdb=" CB ILE B 110 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ARG B 112 " pdb=" N ARG B 112 " pdb=" C ARG B 112 " pdb=" CB ARG B 112 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 1146 not shown) Planarity restraints: 2228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 73 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C CYS A 73 " 0.046 2.00e-02 2.50e+03 pdb=" O CYS A 73 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 74 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 120 " 0.012 2.00e-02 2.50e+03 1.96e-02 5.75e+00 pdb=" CG ASN A 120 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 120 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 120 " 0.033 2.00e-02 2.50e+03 pdb="HD21 ASN A 120 " 0.000 2.00e-02 2.50e+03 pdb="HD22 ASN A 120 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 185 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C TYR A 185 " -0.034 2.00e-02 2.50e+03 pdb=" O TYR A 185 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU A 186 " 0.011 2.00e-02 2.50e+03 ... (remaining 2225 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 546 2.17 - 2.78: 29742 2.78 - 3.38: 42711 3.38 - 3.99: 53391 3.99 - 4.60: 86105 Nonbonded interactions: 212495 Sorted by model distance: nonbonded pdb=" OE1 GLU A 246 " pdb=" H ILE A 249 " model vdw 1.560 2.450 nonbonded pdb=" O THR A 277 " pdb=" HG SER A 280 " model vdw 1.560 2.450 nonbonded pdb=" O GLU A 158 " pdb="HH21 ARG A 166 " model vdw 1.568 2.450 nonbonded pdb="HD21 ASN A 136 " pdb=" O TRP A 179 " model vdw 1.597 2.450 nonbonded pdb=" O VAL A 139 " pdb=" H HIS A 266 " model vdw 1.619 2.450 ... (remaining 212490 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: 1.230 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: 0.090 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.320 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 7787 Z= 0.158 Angle : 0.563 14.399 10542 Z= 0.288 Chirality : 0.037 0.250 1149 Planarity : 0.004 0.039 1348 Dihedral : 13.501 88.452 2907 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.84 % Favored : 96.94 % Rotamer: Outliers : 0.12 % Allowed : 6.58 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.52 (0.29), residues: 915 helix: 1.61 (0.22), residues: 569 sheet: -2.10 (1.17), residues: 16 loop : 0.24 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.009 0.001 TYR A 228 PHE 0.013 0.001 PHE A 417 TRP 0.014 0.001 TRP A 638 HIS 0.006 0.001 HIS D 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 ( 7787) covalent geometry : angle 0.56348 / 0.29 (10542) hydrogen bonds : bond 0.11957 / 8.58 ( 470) hydrogen bonds : angle 5.05895 / 3.54 ( 1344) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.9188 (ttm) cc_final: 0.8675 (ttp) REVERT: A 242 ASP cc_start: 0.8954 (m-30) cc_final: 0.8654 (t0) REVERT: A 371 MET cc_start: 0.9436 (tmm) cc_final: 0.9169 (tmm) REVERT: A 400 MET cc_start: 0.9356 (mmm) cc_final: 0.9123 (mmm) REVERT: A 432 ASP cc_start: 0.9043 (m-30) cc_final: 0.8716 (m-30) REVERT: B 54 GLU cc_start: 0.8948 (mp0) cc_final: 0.8570 (mp0) REVERT: B 95 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8849 (mt-10) outliers start: 1 outliers final: 1 residues processed: 161 average time/residue: 0.2866 time to fit residues: 57.4761 Evaluate side-chains 73 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 649 ASN A 715 GLN B 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.061218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.047117 restraints weight = 84561.944| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.98 r_work: 0.2663 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7787 Z= 0.132 Angle : 0.562 12.701 10542 Z= 0.285 Chirality : 0.035 0.153 1149 Planarity : 0.004 0.042 1348 Dihedral : 3.904 45.233 1012 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.84 % Allowed : 10.05 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.28 (0.29), residues: 915 helix: 2.19 (0.22), residues: 597 sheet: -1.86 (1.20), residues: 16 loop : 0.41 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 26 TYR 0.008 0.001 TYR A 228 PHE 0.011 0.001 PHE A 569 TRP 0.009 0.001 TRP A 638 HIS 0.004 0.001 HIS D 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7787) covalent geometry : angle 0.56152 / 0.29 (10542) hydrogen bonds : bond 0.04199 / 2.88 ( 470) hydrogen bonds : angle 4.16074 / 2.93 ( 1344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ASP cc_start: 0.9204 (m-30) cc_final: 0.8772 (t0) REVERT: A 250 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8784 (mp) REVERT: A 371 MET cc_start: 0.9527 (tmm) cc_final: 0.9295 (tmm) REVERT: A 562 SER cc_start: 0.9687 (OUTLIER) cc_final: 0.9448 (p) REVERT: B 95 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8672 (mp0) outliers start: 7 outliers final: 4 residues processed: 84 average time/residue: 0.2251 time to fit residues: 24.6456 Evaluate side-chains 71 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.044182 restraints weight = 88349.392| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 4.09 r_work: 0.2556 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7787 Z= 0.253 Angle : 0.592 12.759 10542 Z= 0.308 Chirality : 0.037 0.143 1149 Planarity : 0.004 0.035 1348 Dihedral : 3.940 46.561 1012 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.44 % Allowed : 10.17 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.38 (0.28), residues: 915 helix: 2.26 (0.21), residues: 598 sheet: -1.70 (1.18), residues: 16 loop : 0.45 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 206 TYR 0.013 0.001 TYR A 228 PHE 0.018 0.002 PHE A 569 TRP 0.013 0.001 TRP A 638 HIS 0.004 0.001 HIS D 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.25 ( 7787) covalent geometry : angle 0.59183 / 0.31 (10542) hydrogen bonds : bond 0.04067 / 2.80 ( 470) hydrogen bonds : angle 4.30125 / 3.03 ( 1344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8304 (tptp) cc_final: 0.8095 (tptp) REVERT: A 242 ASP cc_start: 0.9282 (m-30) cc_final: 0.8856 (t0) REVERT: A 250 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8727 (mp) REVERT: A 371 MET cc_start: 0.9604 (tmm) cc_final: 0.9379 (tmm) REVERT: A 562 SER cc_start: 0.9695 (OUTLIER) cc_final: 0.9437 (p) outliers start: 12 outliers final: 6 residues processed: 81 average time/residue: 0.2088 time to fit residues: 22.0672 Evaluate side-chains 71 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain B residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.045182 restraints weight = 86751.675| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.07 r_work: 0.2602 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7787 Z= 0.127 Angle : 0.535 12.666 10542 Z= 0.268 Chirality : 0.035 0.128 1149 Planarity : 0.004 0.036 1348 Dihedral : 3.739 41.291 1012 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.96 % Allowed : 10.53 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.86 (0.29), residues: 915 helix: 2.62 (0.21), residues: 596 sheet: -1.48 (1.25), residues: 16 loop : 0.69 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 668 TYR 0.007 0.001 TYR A 461 PHE 0.013 0.001 PHE A 104 TRP 0.010 0.001 TRP A 638 HIS 0.003 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 7787) covalent geometry : angle 0.53534 / 0.27 (10542) hydrogen bonds : bond 0.03617 / 2.46 ( 470) hydrogen bonds : angle 3.93688 / 2.76 ( 1344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8294 (tptp) cc_final: 0.8080 (tptp) REVERT: A 60 ASP cc_start: 0.8923 (m-30) cc_final: 0.8136 (t0) REVERT: A 242 ASP cc_start: 0.9269 (m-30) cc_final: 0.8829 (t0) REVERT: A 250 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8746 (mp) outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.2212 time to fit residues: 21.4894 Evaluate side-chains 69 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 138 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.059460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.045417 restraints weight = 85249.076| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.96 r_work: 0.2615 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7787 Z= 0.110 Angle : 0.514 12.687 10542 Z= 0.255 Chirality : 0.034 0.124 1149 Planarity : 0.003 0.035 1348 Dihedral : 3.536 38.429 1011 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.08 % Allowed : 10.41 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.11 (0.29), residues: 915 helix: 2.80 (0.21), residues: 595 sheet: -1.36 (1.30), residues: 16 loop : 0.83 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 194 TYR 0.008 0.001 TYR A 461 PHE 0.020 0.001 PHE A 292 TRP 0.008 0.001 TRP A 416 HIS 0.003 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 7787) covalent geometry : angle 0.51370 / 0.26 (10542) hydrogen bonds : bond 0.03384 / 2.31 ( 470) hydrogen bonds : angle 3.80094 / 2.67 ( 1344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8322 (tptp) cc_final: 0.8105 (tptp) REVERT: A 242 ASP cc_start: 0.9284 (m-30) cc_final: 0.8839 (t0) REVERT: A 250 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8757 (mp) outliers start: 9 outliers final: 8 residues processed: 71 average time/residue: 0.2488 time to fit residues: 23.2480 Evaluate side-chains 70 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 138 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 54 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.059329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.045289 restraints weight = 85646.138| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.98 r_work: 0.2613 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7787 Z= 0.116 Angle : 0.508 12.703 10542 Z= 0.252 Chirality : 0.034 0.123 1149 Planarity : 0.003 0.035 1348 Dihedral : 3.493 36.000 1011 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.32 % Allowed : 10.29 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.23 (0.29), residues: 915 helix: 2.86 (0.21), residues: 598 sheet: -1.25 (1.31), residues: 16 loop : 0.92 (0.39), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.008 0.001 TYR A 461 PHE 0.017 0.001 PHE A 104 TRP 0.008 0.001 TRP A 638 HIS 0.003 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 7787) covalent geometry : angle 0.50846 / 0.25 (10542) hydrogen bonds : bond 0.03277 / 2.24 ( 470) hydrogen bonds : angle 3.76513 / 2.65 ( 1344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8350 (tptp) cc_final: 0.8121 (tptp) REVERT: A 60 ASP cc_start: 0.8923 (m-30) cc_final: 0.8012 (t0) REVERT: A 242 ASP cc_start: 0.9279 (m-30) cc_final: 0.8827 (t0) REVERT: A 250 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8773 (mp) REVERT: A 371 MET cc_start: 0.9475 (tmm) cc_final: 0.9266 (tmm) outliers start: 11 outliers final: 7 residues processed: 73 average time/residue: 0.2425 time to fit residues: 23.3232 Evaluate side-chains 70 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 138 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 34 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.059569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.045433 restraints weight = 84440.775| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.98 r_work: 0.2618 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7787 Z= 0.101 Angle : 0.506 12.683 10542 Z= 0.248 Chirality : 0.034 0.123 1149 Planarity : 0.003 0.034 1348 Dihedral : 3.442 33.776 1011 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.84 % Allowed : 11.12 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.40 (0.29), residues: 915 helix: 3.04 (0.21), residues: 586 sheet: -1.03 (1.31), residues: 16 loop : 0.97 (0.39), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 610 TYR 0.009 0.001 TYR A 461 PHE 0.015 0.001 PHE A 104 TRP 0.007 0.001 TRP A 416 HIS 0.002 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 7787) covalent geometry : angle 0.50574 / 0.25 (10542) hydrogen bonds : bond 0.03168 / 2.16 ( 470) hydrogen bonds : angle 3.68648 / 2.60 ( 1344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8354 (tptp) cc_final: 0.8124 (tptp) REVERT: A 242 ASP cc_start: 0.9288 (m-30) cc_final: 0.8831 (t0) REVERT: A 250 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8777 (mp) REVERT: A 752 LEU cc_start: 0.9546 (mt) cc_final: 0.9243 (mt) outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 0.2337 time to fit residues: 20.9768 Evaluate side-chains 68 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 138 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.059777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.045538 restraints weight = 85594.661| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 4.05 r_work: 0.2625 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7787 Z= 0.098 Angle : 0.511 12.697 10542 Z= 0.250 Chirality : 0.034 0.127 1149 Planarity : 0.003 0.033 1348 Dihedral : 3.409 32.930 1011 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.08 % Allowed : 10.89 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.51 (0.29), residues: 915 helix: 3.08 (0.21), residues: 592 sheet: -0.88 (1.31), residues: 16 loop : 1.06 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 401 TYR 0.010 0.001 TYR A 461 PHE 0.016 0.001 PHE A 104 TRP 0.007 0.001 TRP A 416 HIS 0.002 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 7787) covalent geometry : angle 0.51110 / 0.25 (10542) hydrogen bonds : bond 0.03087 / 2.11 ( 470) hydrogen bonds : angle 3.64123 / 2.56 ( 1344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8355 (tptp) cc_final: 0.8123 (tptp) REVERT: A 60 ASP cc_start: 0.8932 (m-30) cc_final: 0.8049 (t0) REVERT: A 242 ASP cc_start: 0.9268 (m-30) cc_final: 0.8810 (t0) REVERT: A 250 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8768 (mp) REVERT: A 752 LEU cc_start: 0.9537 (mt) cc_final: 0.9155 (mt) REVERT: B 46 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8093 (t0) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.2508 time to fit residues: 22.2972 Evaluate side-chains 68 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 138 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 22 optimal weight: 0.0270 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.058460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.044395 restraints weight = 85745.647| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.98 r_work: 0.2592 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7787 Z= 0.165 Angle : 0.533 12.850 10542 Z= 0.268 Chirality : 0.035 0.121 1149 Planarity : 0.003 0.032 1348 Dihedral : 3.522 34.532 1011 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.44 % Allowed : 10.77 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.33 (0.29), residues: 915 helix: 2.93 (0.21), residues: 597 sheet: -0.78 (1.25), residues: 16 loop : 0.97 (0.40), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 206 TYR 0.009 0.001 TYR A 228 PHE 0.016 0.001 PHE A 104 TRP 0.008 0.001 TRP A 638 HIS 0.003 0.001 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 ( 7787) covalent geometry : angle 0.53306 / 0.27 (10542) hydrogen bonds : bond 0.03276 / 2.25 ( 470) hydrogen bonds : angle 3.80086 / 2.68 ( 1344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8409 (tptp) cc_final: 0.8166 (tptp) REVERT: A 60 ASP cc_start: 0.8959 (m-30) cc_final: 0.8183 (t0) REVERT: A 242 ASP cc_start: 0.9300 (m-30) cc_final: 0.8837 (t0) REVERT: A 250 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8776 (mp) REVERT: B 46 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8258 (t0) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.2538 time to fit residues: 22.1779 Evaluate side-chains 66 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 138 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.058822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.044875 restraints weight = 85910.525| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.95 r_work: 0.2602 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7787 Z= 0.128 Angle : 0.525 12.688 10542 Z= 0.260 Chirality : 0.035 0.187 1149 Planarity : 0.003 0.033 1348 Dihedral : 3.494 33.582 1011 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.56 % Allowed : 10.77 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.40 (0.29), residues: 915 helix: 2.97 (0.21), residues: 597 sheet: -0.60 (1.25), residues: 16 loop : 1.03 (0.40), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 610 TYR 0.009 0.001 TYR A 461 PHE 0.015 0.001 PHE A 104 TRP 0.008 0.001 TRP A 416 HIS 0.002 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 7787) covalent geometry : angle 0.52511 / 0.26 (10542) hydrogen bonds : bond 0.03198 / 2.19 ( 470) hydrogen bonds : angle 3.72151 / 2.61 ( 1344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8435 (tptp) cc_final: 0.8190 (tptp) REVERT: A 60 ASP cc_start: 0.8976 (m-30) cc_final: 0.8176 (t0) REVERT: A 242 ASP cc_start: 0.9304 (m-30) cc_final: 0.8838 (t0) REVERT: A 250 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8797 (mp) REVERT: B 46 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8240 (t0) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.2443 time to fit residues: 22.3129 Evaluate side-chains 72 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 138 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.059249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.045431 restraints weight = 85031.685| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.95 r_work: 0.2623 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7787 Z= 0.100 Angle : 0.513 12.798 10542 Z= 0.251 Chirality : 0.034 0.167 1149 Planarity : 0.003 0.033 1348 Dihedral : 3.428 33.288 1011 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.32 % Allowed : 11.12 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.54 (0.29), residues: 915 helix: 3.07 (0.21), residues: 597 sheet: -0.58 (1.27), residues: 16 loop : 1.11 (0.40), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 610 TYR 0.010 0.001 TYR A 461 PHE 0.014 0.001 PHE A 104 TRP 0.008 0.001 TRP A 416 HIS 0.002 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 7787) covalent geometry : angle 0.51314 / 0.25 (10542) hydrogen bonds : bond 0.03049 / 2.08 ( 470) hydrogen bonds : angle 3.61135 / 2.54 ( 1344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3026.75 seconds wall clock time: 52 minutes 16.05 seconds (3136.05 seconds total)