Starting phenix.real_space_refine on Tue Mar 3 13:51:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r1y_14243/03_2026/7r1y_14243.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r1y_14243/03_2026/7r1y_14243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r1y_14243/03_2026/7r1y_14243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r1y_14243/03_2026/7r1y_14243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r1y_14243/03_2026/7r1y_14243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r1y_14243/03_2026/7r1y_14243.map" } resolution = 3.0 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= 0.001 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 33 5.16 5 C 3615 2.51 5 N 982 2.21 5 O 1074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5704 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5704 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 689} Chain breaks: 11 Time building chain proxies: 1.24, per 1000 atoms: 0.22 Number of scatterers: 5704 At special positions: 0 Unit cell: (71.9488, 74.752, 122.406, 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 33 16.00 O 1074 8.00 N 982 7.00 C 3615 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: 0.45 Conformation dependent library (CDL) restraints added in 341.7 milliseconds 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 43.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 19 through 37 removed outlier: 3.679A pdb=" N ARG A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.633A pdb=" N GLN A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.522A pdb=" N VAL A 324 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 326 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.781A pdb=" N SER A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 513 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 529 through 542 Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 647 through 661 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 689 through 710 Processing helix chain 'A' and resid 761 through 787 Processing helix chain 'A' and resid 788 through 795 Processing helix chain 'A' and resid 797 through 806 removed outlier: 3.605A pdb=" N ILE A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 814 Processing helix chain 'A' and resid 818 through 834 removed outlier: 3.534A pdb=" N ASP A 834 " --> pdb=" O CYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 849 Processing helix chain 'A' and resid 854 through 870 Processing helix chain 'A' and resid 875 through 892 removed outlier: 3.620A pdb=" N LYS A 879 " --> pdb=" O ASN A 875 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 880 " --> pdb=" O LYS A 876 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 881 " --> pdb=" O THR A 877 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 882 " --> pdb=" O GLU A 878 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.516A pdb=" N VAL A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 927 removed outlier: 3.589A pdb=" N ASP A 927 " --> pdb=" O ALA A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 967 removed outlier: 3.552A pdb=" N CYS A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.797A pdb=" N TYR A 355 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL A 376 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG A 353 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 88 removed outlier: 3.546A pdb=" N ALA A 446 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.584A pdb=" N GLY A 107 " --> pdb=" O TRP A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 150 Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 220 removed outlier: 6.627A pdb=" N ALA A 229 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 218 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE A 227 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE A 226 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 271 removed outlier: 3.694A pdb=" N GLN A 267 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A 287 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 286 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER A 303 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 288 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 400 removed outlier: 3.707A pdb=" N ARG A 396 " --> pdb=" O ALA A 407 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1895 1.34 - 1.46: 1156 1.46 - 1.58: 2701 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 5801 Sorted by residual: bond pdb=" C PRO A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.23e+00 bond pdb=" C VAL A 897 " pdb=" N ASP A 898 " ideal model delta sigma weight residual 1.328 1.340 -0.012 1.30e-02 5.92e+03 9.08e-01 bond pdb=" CA SER A 83 " pdb=" C SER A 83 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.29e-01 bond pdb=" C ALA A 229 " pdb=" N GLY A 230 " ideal model delta sigma weight residual 1.331 1.319 0.012 1.46e-02 4.69e+03 6.71e-01 bond pdb=" CA PRO A 110 " pdb=" C PRO A 110 " ideal model delta sigma weight residual 1.517 1.524 -0.007 9.30e-03 1.16e+04 6.23e-01 ... (remaining 5796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 7744 1.80 - 3.60: 96 3.60 - 5.40: 9 5.40 - 7.19: 2 7.19 - 8.99: 1 Bond angle restraints: 7852 Sorted by residual: angle pdb=" N ILE A 893 " pdb=" CA ILE A 893 " pdb=" C ILE A 893 " ideal model delta sigma weight residual 113.20 109.80 3.40 9.60e-01 1.09e+00 1.25e+01 angle pdb=" C VAL A 897 " pdb=" N ASP A 898 " pdb=" CA ASP A 898 " ideal model delta sigma weight residual 122.82 127.52 -4.70 1.42e+00 4.96e-01 1.10e+01 angle pdb=" C SER A 83 " pdb=" N ILE A 84 " pdb=" CA ILE A 84 " ideal model delta sigma weight residual 122.93 119.05 3.88 1.21e+00 6.83e-01 1.03e+01 angle pdb=" N ASP A 898 " pdb=" CA ASP A 898 " pdb=" C ASP A 898 " ideal model delta sigma weight residual 111.17 115.52 -4.35 1.41e+00 5.03e-01 9.51e+00 angle pdb=" N PRO A 110 " pdb=" CA PRO A 110 " pdb=" C PRO A 110 " ideal model delta sigma weight residual 110.70 114.00 -3.30 1.22e+00 6.72e-01 7.33e+00 ... (remaining 7847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 3267 17.24 - 34.47: 189 34.47 - 51.71: 80 51.71 - 68.94: 8 68.94 - 86.18: 4 Dihedral angle restraints: 3548 sinusoidal: 1438 harmonic: 2110 Sorted by residual: dihedral pdb=" CA HIS A 349 " pdb=" C HIS A 349 " pdb=" N ALA A 350 " pdb=" CA ALA A 350 " ideal model delta harmonic sigma weight residual -180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PRO A 468 " pdb=" C PRO A 468 " pdb=" N ILE A 469 " pdb=" CA ILE A 469 " ideal model delta harmonic sigma weight residual -180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ILE A 469 " pdb=" C ILE A 469 " pdb=" N THR A 470 " pdb=" CA THR A 470 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 539 0.027 - 0.054: 225 0.054 - 0.081: 86 0.081 - 0.108: 37 0.108 - 0.135: 24 Chirality restraints: 911 Sorted by residual: chirality pdb=" CA ILE A 218 " pdb=" N ILE A 218 " pdb=" C ILE A 218 " pdb=" CB ILE A 218 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CG LEU A 228 " pdb=" CB LEU A 228 " pdb=" CD1 LEU A 228 " pdb=" CD2 LEU A 228 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A 416 " pdb=" N ILE A 416 " pdb=" C ILE A 416 " pdb=" CB ILE A 416 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 908 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 51 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 52 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 110 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 111 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 472 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 473 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.022 5.00e-02 4.00e+02 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1103 2.78 - 3.31: 5462 3.31 - 3.84: 9467 3.84 - 4.37: 11138 4.37 - 4.90: 19024 Nonbonded interactions: 46194 Sorted by model distance: nonbonded pdb=" N LEU A 145 " pdb=" O ALA A 168 " model vdw 2.252 3.120 nonbonded pdb=" OG1 THR A 169 " pdb=" O ASP A 172 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLN A 287 " pdb=" OH TYR A 289 " model vdw 2.334 3.040 nonbonded pdb=" OE1 GLN A 891 " pdb=" OG1 THR A 921 " model vdw 2.353 3.040 nonbonded pdb=" OD2 ASP A 232 " pdb=" OH TYR A 236 " model vdw 2.361 3.040 ... (remaining 46189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.370 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 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 : 0.002 0.039 5801 Z= 0.115 Angle : 0.524 8.992 7852 Z= 0.293 Chirality : 0.041 0.135 911 Planarity : 0.004 0.046 1008 Dihedral : 13.126 86.178 2170 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.44 % Allowed : 11.42 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.36 (0.32), residues: 699 helix: 1.36 (0.31), residues: 286 sheet: -0.03 (0.42), residues: 156 loop : -0.79 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 501 TYR 0.007 0.001 TYR A 206 PHE 0.014 0.001 PHE A 497 TRP 0.008 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 5801) covalent geometry : angle 0.52371 ( 7852) hydrogen bonds : bond 0.12620 ( 283) hydrogen bonds : angle 5.25988 ( 801) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.3986 (OUTLIER) cc_final: 0.3625 (t80) REVERT: A 806 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7314 (tt) REVERT: A 855 THR cc_start: 0.7815 (p) cc_final: 0.7477 (t) REVERT: A 962 THR cc_start: 0.6266 (m) cc_final: 0.5904 (p) outliers start: 22 outliers final: 8 residues processed: 128 average time/residue: 0.4336 time to fit residues: 58.3031 Evaluate side-chains 69 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN A 891 GLN ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.171470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.149353 restraints weight = 9152.937| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.88 r_work: 0.3886 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5801 Z= 0.151 Angle : 0.598 9.336 7852 Z= 0.308 Chirality : 0.042 0.167 911 Planarity : 0.005 0.041 1008 Dihedral : 6.403 53.214 787 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.79 % Allowed : 16.28 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.67 (0.32), residues: 699 helix: 1.77 (0.31), residues: 286 sheet: 0.02 (0.43), residues: 148 loop : -0.73 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 501 TYR 0.012 0.001 TYR A 128 PHE 0.012 0.002 PHE A 497 TRP 0.010 0.001 TRP A 116 HIS 0.005 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 5801) covalent geometry : angle 0.59786 ( 7852) hydrogen bonds : bond 0.03879 ( 283) hydrogen bonds : angle 4.36063 ( 801) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 0.257 Fit side-chains REVERT: A 39 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.6022 (pmt) REVERT: A 157 PHE cc_start: 0.4211 (OUTLIER) cc_final: 0.3704 (t80) REVERT: A 691 GLN cc_start: 0.7391 (tp40) cc_final: 0.7073 (tp40) REVERT: A 780 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6493 (tt) REVERT: A 806 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7298 (tt) REVERT: A 855 THR cc_start: 0.7912 (p) cc_final: 0.7654 (t) REVERT: A 911 PHE cc_start: 0.7244 (t80) cc_final: 0.6782 (t80) REVERT: A 962 THR cc_start: 0.6291 (m) cc_final: 0.5923 (p) outliers start: 37 outliers final: 14 residues processed: 98 average time/residue: 0.4001 time to fit residues: 41.4687 Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 897 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN A 864 ASN A 868 GLN ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.173502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.151681 restraints weight = 9056.925| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.89 r_work: 0.3915 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5801 Z= 0.113 Angle : 0.543 8.078 7852 Z= 0.276 Chirality : 0.041 0.180 911 Planarity : 0.004 0.039 1008 Dihedral : 5.864 50.996 784 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 6.26 % Allowed : 16.74 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.89 (0.32), residues: 699 helix: 1.99 (0.31), residues: 287 sheet: 0.09 (0.43), residues: 148 loop : -0.65 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 501 TYR 0.018 0.001 TYR A 775 PHE 0.012 0.001 PHE A 497 TRP 0.008 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5801) covalent geometry : angle 0.54320 ( 7852) hydrogen bonds : bond 0.03315 ( 283) hydrogen bonds : angle 4.09350 ( 801) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 65 time to evaluate : 0.203 Fit side-chains REVERT: A 105 MET cc_start: 0.7498 (mtt) cc_final: 0.7195 (mtp) REVERT: A 157 PHE cc_start: 0.4114 (OUTLIER) cc_final: 0.3743 (t80) REVERT: A 780 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6448 (tt) REVERT: A 806 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7236 (tt) REVERT: A 855 THR cc_start: 0.7930 (p) cc_final: 0.7693 (t) REVERT: A 906 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.5965 (m-10) REVERT: A 912 TYR cc_start: 0.5000 (OUTLIER) cc_final: 0.4177 (p90) REVERT: A 962 THR cc_start: 0.6276 (m) cc_final: 0.5900 (p) outliers start: 40 outliers final: 14 residues processed: 95 average time/residue: 0.3860 time to fit residues: 38.9176 Evaluate side-chains 75 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 37 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.173344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.151628 restraints weight = 9046.955| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.88 r_work: 0.3911 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5801 Z= 0.119 Angle : 0.549 7.473 7852 Z= 0.282 Chirality : 0.042 0.198 911 Planarity : 0.004 0.038 1008 Dihedral : 5.707 50.511 782 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.79 % Allowed : 18.00 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.92 (0.32), residues: 699 helix: 2.02 (0.31), residues: 287 sheet: 0.10 (0.43), residues: 148 loop : -0.63 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 501 TYR 0.020 0.001 TYR A 775 PHE 0.012 0.001 PHE A 497 TRP 0.008 0.001 TRP A 116 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 5801) covalent geometry : angle 0.54910 ( 7852) hydrogen bonds : bond 0.03224 ( 283) hydrogen bonds : angle 4.00894 ( 801) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.207 Fit side-chains REVERT: A 25 ASN cc_start: 0.6258 (t0) cc_final: 0.6018 (m-40) REVERT: A 105 MET cc_start: 0.7440 (mtt) cc_final: 0.7200 (mtm) REVERT: A 157 PHE cc_start: 0.4175 (OUTLIER) cc_final: 0.3710 (t80) REVERT: A 467 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7009 (mt) REVERT: A 780 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6436 (tt) REVERT: A 855 THR cc_start: 0.7847 (p) cc_final: 0.7559 (t) REVERT: A 884 ARG cc_start: 0.8166 (mpt180) cc_final: 0.7962 (mpt-90) REVERT: A 906 TYR cc_start: 0.6147 (m-80) cc_final: 0.5930 (m-10) REVERT: A 912 TYR cc_start: 0.4956 (OUTLIER) cc_final: 0.4240 (p90) REVERT: A 962 THR cc_start: 0.6260 (m) cc_final: 0.5879 (p) outliers start: 37 outliers final: 18 residues processed: 95 average time/residue: 0.3841 time to fit residues: 38.8469 Evaluate side-chains 80 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.172014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.150081 restraints weight = 9198.018| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.92 r_work: 0.3889 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5801 Z= 0.139 Angle : 0.582 11.665 7852 Z= 0.297 Chirality : 0.043 0.212 911 Planarity : 0.004 0.038 1008 Dihedral : 5.413 51.391 778 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.48 % Allowed : 19.56 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.92 (0.32), residues: 699 helix: 2.02 (0.31), residues: 287 sheet: 0.07 (0.44), residues: 148 loop : -0.60 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 501 TYR 0.008 0.001 TYR A 136 PHE 0.011 0.001 PHE A 497 TRP 0.011 0.001 TRP A 116 HIS 0.005 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5801) covalent geometry : angle 0.58220 ( 7852) hydrogen bonds : bond 0.03432 ( 283) hydrogen bonds : angle 4.10839 ( 801) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 0.206 Fit side-chains REVERT: A 25 ASN cc_start: 0.6314 (t0) cc_final: 0.6067 (m-40) REVERT: A 105 MET cc_start: 0.7507 (mtt) cc_final: 0.7241 (mtm) REVERT: A 136 TYR cc_start: 0.4976 (OUTLIER) cc_final: 0.4626 (p90) REVERT: A 157 PHE cc_start: 0.4194 (OUTLIER) cc_final: 0.3657 (t80) REVERT: A 232 ASP cc_start: 0.7565 (p0) cc_final: 0.7343 (p0) REVERT: A 780 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6487 (tt) REVERT: A 855 THR cc_start: 0.7904 (p) cc_final: 0.7616 (t) REVERT: A 884 ARG cc_start: 0.8139 (mpt180) cc_final: 0.7939 (mpt-90) REVERT: A 906 TYR cc_start: 0.6208 (m-80) cc_final: 0.5949 (m-10) REVERT: A 912 TYR cc_start: 0.5084 (OUTLIER) cc_final: 0.4652 (p90) REVERT: A 962 THR cc_start: 0.6272 (m) cc_final: 0.5908 (p) outliers start: 35 outliers final: 21 residues processed: 91 average time/residue: 0.3797 time to fit residues: 36.8703 Evaluate side-chains 79 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.173003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.151201 restraints weight = 9092.870| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.89 r_work: 0.3900 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5801 Z= 0.120 Angle : 0.566 7.654 7852 Z= 0.288 Chirality : 0.042 0.187 911 Planarity : 0.004 0.039 1008 Dihedral : 5.312 50.153 778 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.48 % Allowed : 20.19 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.02 (0.33), residues: 699 helix: 2.11 (0.31), residues: 287 sheet: 0.05 (0.44), residues: 149 loop : -0.51 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 367 TYR 0.007 0.001 TYR A 128 PHE 0.012 0.001 PHE A 497 TRP 0.013 0.001 TRP A 116 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 5801) covalent geometry : angle 0.56550 ( 7852) hydrogen bonds : bond 0.03224 ( 283) hydrogen bonds : angle 4.03499 ( 801) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 0.173 Fit side-chains REVERT: A 25 ASN cc_start: 0.6286 (t0) cc_final: 0.6058 (m-40) REVERT: A 105 MET cc_start: 0.7479 (mtt) cc_final: 0.7203 (mtm) REVERT: A 136 TYR cc_start: 0.4909 (OUTLIER) cc_final: 0.4598 (p90) REVERT: A 157 PHE cc_start: 0.4200 (OUTLIER) cc_final: 0.3682 (t80) REVERT: A 232 ASP cc_start: 0.7598 (p0) cc_final: 0.7360 (p0) REVERT: A 780 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6550 (tt) REVERT: A 855 THR cc_start: 0.7823 (p) cc_final: 0.7535 (t) REVERT: A 895 ASN cc_start: 0.6611 (OUTLIER) cc_final: 0.6111 (m-40) REVERT: A 906 TYR cc_start: 0.6139 (m-80) cc_final: 0.5767 (m-10) REVERT: A 912 TYR cc_start: 0.4904 (OUTLIER) cc_final: 0.4449 (p90) REVERT: A 962 THR cc_start: 0.6501 (m) cc_final: 0.6123 (p) outliers start: 35 outliers final: 21 residues processed: 90 average time/residue: 0.3703 time to fit residues: 35.5039 Evaluate side-chains 81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 71 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.171857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.150060 restraints weight = 9139.031| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.90 r_work: 0.3886 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5801 Z= 0.140 Angle : 0.589 11.559 7852 Z= 0.299 Chirality : 0.044 0.323 911 Planarity : 0.004 0.040 1008 Dihedral : 5.414 51.072 778 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.16 % Allowed : 21.13 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.90 (0.32), residues: 699 helix: 1.96 (0.31), residues: 287 sheet: 0.03 (0.44), residues: 148 loop : -0.54 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.009 0.001 TYR A 136 PHE 0.011 0.001 PHE A 497 TRP 0.017 0.002 TRP A 116 HIS 0.005 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5801) covalent geometry : angle 0.58906 ( 7852) hydrogen bonds : bond 0.03434 ( 283) hydrogen bonds : angle 4.15528 ( 801) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.225 Fit side-chains REVERT: A 25 ASN cc_start: 0.6285 (t0) cc_final: 0.6062 (m-40) REVERT: A 105 MET cc_start: 0.7466 (mtt) cc_final: 0.7229 (mtm) REVERT: A 136 TYR cc_start: 0.4986 (OUTLIER) cc_final: 0.4591 (p90) REVERT: A 157 PHE cc_start: 0.4183 (OUTLIER) cc_final: 0.3646 (t80) REVERT: A 232 ASP cc_start: 0.7512 (p0) cc_final: 0.7290 (p0) REVERT: A 771 VAL cc_start: 0.7446 (p) cc_final: 0.7246 (t) REVERT: A 780 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6290 (tt) REVERT: A 855 THR cc_start: 0.7867 (p) cc_final: 0.7574 (t) REVERT: A 884 ARG cc_start: 0.8092 (tpp-160) cc_final: 0.7740 (mpt-90) REVERT: A 895 ASN cc_start: 0.6690 (OUTLIER) cc_final: 0.6184 (m-40) REVERT: A 912 TYR cc_start: 0.4858 (OUTLIER) cc_final: 0.4453 (p90) REVERT: A 962 THR cc_start: 0.6507 (m) cc_final: 0.6128 (p) outliers start: 33 outliers final: 20 residues processed: 91 average time/residue: 0.3873 time to fit residues: 37.4383 Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.172667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.150945 restraints weight = 9104.824| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.89 r_work: 0.3897 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5801 Z= 0.129 Angle : 0.582 9.807 7852 Z= 0.295 Chirality : 0.043 0.205 911 Planarity : 0.004 0.041 1008 Dihedral : 5.384 50.805 778 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.69 % Allowed : 21.60 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.90 (0.32), residues: 699 helix: 1.95 (0.31), residues: 287 sheet: -0.03 (0.44), residues: 149 loop : -0.48 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 252 TYR 0.008 0.001 TYR A 775 PHE 0.012 0.001 PHE A 497 TRP 0.008 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5801) covalent geometry : angle 0.58171 ( 7852) hydrogen bonds : bond 0.03341 ( 283) hydrogen bonds : angle 4.14740 ( 801) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.226 Fit side-chains REVERT: A 25 ASN cc_start: 0.6243 (t0) cc_final: 0.6026 (m-40) REVERT: A 136 TYR cc_start: 0.5001 (OUTLIER) cc_final: 0.4631 (p90) REVERT: A 157 PHE cc_start: 0.4245 (OUTLIER) cc_final: 0.3698 (t80) REVERT: A 232 ASP cc_start: 0.7519 (p0) cc_final: 0.7299 (p0) REVERT: A 467 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.6997 (mt) REVERT: A 771 VAL cc_start: 0.7445 (p) cc_final: 0.7203 (t) REVERT: A 780 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6322 (tt) REVERT: A 855 THR cc_start: 0.7859 (p) cc_final: 0.7562 (t) REVERT: A 884 ARG cc_start: 0.8091 (tpp-160) cc_final: 0.7751 (mpt-90) REVERT: A 895 ASN cc_start: 0.6692 (OUTLIER) cc_final: 0.6212 (m-40) REVERT: A 906 TYR cc_start: 0.6100 (OUTLIER) cc_final: 0.5718 (m-10) REVERT: A 962 THR cc_start: 0.6514 (m) cc_final: 0.6135 (p) outliers start: 30 outliers final: 18 residues processed: 85 average time/residue: 0.3778 time to fit residues: 34.1456 Evaluate side-chains 81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.174559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.152862 restraints weight = 9046.769| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.90 r_work: 0.3920 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5801 Z= 0.114 Angle : 0.569 10.194 7852 Z= 0.286 Chirality : 0.043 0.215 911 Planarity : 0.004 0.040 1008 Dihedral : 5.215 50.951 778 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.23 % Allowed : 22.69 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.05 (0.33), residues: 699 helix: 2.06 (0.31), residues: 287 sheet: 0.08 (0.45), residues: 149 loop : -0.42 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 252 TYR 0.007 0.001 TYR A 775 PHE 0.012 0.001 PHE A 497 TRP 0.011 0.001 TRP A 116 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5801) covalent geometry : angle 0.56903 ( 7852) hydrogen bonds : bond 0.03177 ( 283) hydrogen bonds : angle 4.06256 ( 801) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.207 Fit side-chains REVERT: A 25 ASN cc_start: 0.6302 (t0) cc_final: 0.6075 (m-40) REVERT: A 117 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6963 (tt) REVERT: A 157 PHE cc_start: 0.4129 (OUTLIER) cc_final: 0.3696 (t80) REVERT: A 467 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.6976 (mt) REVERT: A 771 VAL cc_start: 0.7429 (p) cc_final: 0.7223 (t) REVERT: A 780 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6269 (tt) REVERT: A 855 THR cc_start: 0.7780 (p) cc_final: 0.7530 (t) REVERT: A 884 ARG cc_start: 0.8095 (tpp-160) cc_final: 0.7775 (mpt-90) REVERT: A 895 ASN cc_start: 0.6782 (OUTLIER) cc_final: 0.6318 (m-40) REVERT: A 906 TYR cc_start: 0.5980 (OUTLIER) cc_final: 0.5562 (m-10) REVERT: A 962 THR cc_start: 0.6455 (m) cc_final: 0.6091 (p) outliers start: 27 outliers final: 14 residues processed: 84 average time/residue: 0.3952 time to fit residues: 35.2046 Evaluate side-chains 76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 31 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.174193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.152868 restraints weight = 9185.841| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.88 r_work: 0.3921 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5801 Z= 0.118 Angle : 0.586 10.773 7852 Z= 0.298 Chirality : 0.043 0.232 911 Planarity : 0.004 0.040 1008 Dihedral : 4.940 51.163 776 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.29 % Allowed : 23.94 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.04 (0.32), residues: 699 helix: 2.05 (0.31), residues: 287 sheet: 0.05 (0.44), residues: 149 loop : -0.38 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 252 TYR 0.011 0.001 TYR A 775 PHE 0.012 0.001 PHE A 497 TRP 0.010 0.001 TRP A 116 HIS 0.004 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 5801) covalent geometry : angle 0.58578 ( 7852) hydrogen bonds : bond 0.03186 ( 283) hydrogen bonds : angle 4.03875 ( 801) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.213 Fit side-chains REVERT: A 25 ASN cc_start: 0.6197 (t0) cc_final: 0.5962 (m-40) REVERT: A 117 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6946 (tt) REVERT: A 157 PHE cc_start: 0.4206 (OUTLIER) cc_final: 0.3721 (t80) REVERT: A 467 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.6959 (mt) REVERT: A 691 GLN cc_start: 0.7167 (tp40) cc_final: 0.6259 (pm20) REVERT: A 771 VAL cc_start: 0.7411 (p) cc_final: 0.7206 (t) REVERT: A 780 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6225 (tt) REVERT: A 855 THR cc_start: 0.7760 (p) cc_final: 0.7481 (t) REVERT: A 884 ARG cc_start: 0.8135 (tpp-160) cc_final: 0.7823 (mpt-90) REVERT: A 895 ASN cc_start: 0.6701 (OUTLIER) cc_final: 0.6223 (m-40) REVERT: A 906 TYR cc_start: 0.6032 (OUTLIER) cc_final: 0.5616 (m-10) REVERT: A 962 THR cc_start: 0.6484 (m) cc_final: 0.6126 (p) outliers start: 21 outliers final: 14 residues processed: 76 average time/residue: 0.3923 time to fit residues: 31.7070 Evaluate side-chains 75 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.172349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.150693 restraints weight = 9022.717| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.87 r_work: 0.3895 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5801 Z= 0.142 Angle : 0.608 10.454 7852 Z= 0.312 Chirality : 0.044 0.224 911 Planarity : 0.004 0.041 1008 Dihedral : 5.135 52.546 776 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.07 % Allowed : 23.32 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.90 (0.32), residues: 699 helix: 1.90 (0.31), residues: 287 sheet: -0.02 (0.44), residues: 149 loop : -0.43 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 252 TYR 0.011 0.001 TYR A 775 PHE 0.012 0.001 PHE A 497 TRP 0.007 0.001 TRP A 116 HIS 0.005 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5801) covalent geometry : angle 0.60807 ( 7852) hydrogen bonds : bond 0.03459 ( 283) hydrogen bonds : angle 4.19831 ( 801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1891.59 seconds wall clock time: 33 minutes 0.56 seconds (1980.56 seconds total)