Starting phenix.real_space_refine on Tue Feb 11 12:07:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r1y_14243/02_2025/7r1y_14243.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r1y_14243/02_2025/7r1y_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7r1y_14243/02_2025/7r1y_14243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r1y_14243/02_2025/7r1y_14243.map" model { file = "/net/cci-nas-00/data/ceres_data/7r1y_14243/02_2025/7r1y_14243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r1y_14243/02_2025/7r1y_14243.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.56, per 1000 atoms: 0.62 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: 1.46 Conformation dependent library (CDL) restraints added in 904.5 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: 0.65 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: 1.97 Time building geometry restraints manager: 1.70 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: 0.400 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.280 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.350 ------------------------------------------------------------------------------- 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= 0.157 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (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 TRP 0.008 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.014 0.001 PHE A 497 TYR 0.007 0.001 TYR A 206 ARG 0.003 0.000 ARG A 501 *********************** 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 : 0.667 Fit side-chains REVERT: A 157 PHE cc_start: 0.3986 (OUTLIER) cc_final: 0.3626 (t80) REVERT: A 806 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7312 (tt) REVERT: A 855 THR cc_start: 0.7815 (p) cc_final: 0.7476 (t) REVERT: A 962 THR cc_start: 0.6266 (m) cc_final: 0.5905 (p) outliers start: 22 outliers final: 8 residues processed: 128 average time/residue: 0.9468 time to fit residues: 128.1866 Evaluate side-chains 71 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.172316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.150762 restraints weight = 8998.348| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.88 r_work: 0.3901 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5801 Z= 0.199 Angle : 0.583 9.456 7852 Z= 0.300 Chirality : 0.042 0.164 911 Planarity : 0.005 0.040 1008 Dihedral : 6.292 52.111 787 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.48 % Allowed : 16.43 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.32), residues: 699 helix: 1.88 (0.31), residues: 283 sheet: 0.06 (0.43), residues: 148 loop : -0.66 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.004 0.001 HIS A 498 PHE 0.013 0.001 PHE A 497 TYR 0.013 0.001 TYR A 128 ARG 0.006 0.001 ARG A 501 *********************** 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 105 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.653 Fit side-chains REVERT: A 39 MET cc_start: 0.6229 (ptt) cc_final: 0.6003 (pmt) REVERT: A 157 PHE cc_start: 0.4120 (OUTLIER) cc_final: 0.3687 (t80) REVERT: A 691 GLN cc_start: 0.7377 (tp40) cc_final: 0.7079 (tp40) REVERT: A 780 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6461 (tt) REVERT: A 806 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7286 (tt) REVERT: A 855 THR cc_start: 0.7900 (p) cc_final: 0.7615 (t) REVERT: A 911 PHE cc_start: 0.7230 (t80) cc_final: 0.6943 (t80) REVERT: A 962 THR cc_start: 0.6264 (m) cc_final: 0.5892 (p) outliers start: 35 outliers final: 15 residues processed: 98 average time/residue: 0.9247 time to fit residues: 96.6006 Evaluate side-chains 76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 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 294 ASP 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 48 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 0.0170 chunk 11 optimal weight: 0.9980 overall best weight: 0.9020 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.172881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.151024 restraints weight = 9118.120| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.91 r_work: 0.3905 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5801 Z= 0.178 Angle : 0.549 8.330 7852 Z= 0.281 Chirality : 0.041 0.185 911 Planarity : 0.004 0.039 1008 Dihedral : 5.921 51.592 784 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.95 % Allowed : 17.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.32), residues: 699 helix: 1.98 (0.31), residues: 287 sheet: 0.10 (0.43), residues: 148 loop : -0.65 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 497 TYR 0.020 0.001 TYR A 775 ARG 0.004 0.000 ARG A 501 *********************** 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 101 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 63 time to evaluate : 0.812 Fit side-chains REVERT: A 105 MET cc_start: 0.7475 (mtt) cc_final: 0.7194 (mtp) REVERT: A 157 PHE cc_start: 0.4186 (OUTLIER) cc_final: 0.3763 (t80) REVERT: A 691 GLN cc_start: 0.7384 (tp40) cc_final: 0.7144 (tp40) REVERT: A 780 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6548 (tt) REVERT: A 806 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7254 (tt) REVERT: A 855 THR cc_start: 0.7914 (p) cc_final: 0.7621 (t) REVERT: A 912 TYR cc_start: 0.5033 (OUTLIER) cc_final: 0.4159 (p90) REVERT: A 962 THR cc_start: 0.6276 (m) cc_final: 0.5963 (p) outliers start: 38 outliers final: 16 residues processed: 94 average time/residue: 0.8992 time to fit residues: 90.1124 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 : 0.799 ------------------------------------------------------------------------------- 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 172 ASP 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 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 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 0 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.169454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.147840 restraints weight = 9145.707| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.86 r_work: 0.3863 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5801 Z= 0.249 Angle : 0.593 7.348 7852 Z= 0.308 Chirality : 0.044 0.206 911 Planarity : 0.004 0.039 1008 Dihedral : 5.988 53.938 782 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 6.42 % Allowed : 17.53 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.32), residues: 699 helix: 1.74 (0.31), residues: 287 sheet: -0.02 (0.43), residues: 148 loop : -0.70 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.005 0.001 HIS A 498 PHE 0.012 0.002 PHE A 124 TYR 0.021 0.002 TYR A 775 ARG 0.003 0.000 ARG A 367 *********************** 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 110 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 69 time to evaluate : 0.690 Fit side-chains REVERT: A 25 ASN cc_start: 0.6295 (t0) cc_final: 0.6026 (m-40) REVERT: A 105 MET cc_start: 0.7413 (mtt) cc_final: 0.7073 (mtp) REVERT: A 136 TYR cc_start: 0.5022 (OUTLIER) cc_final: 0.4731 (p90) REVERT: A 691 GLN cc_start: 0.7404 (tp40) cc_final: 0.7162 (tp40) REVERT: A 780 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6637 (tt) REVERT: A 806 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7299 (tt) REVERT: A 855 THR cc_start: 0.7876 (p) cc_final: 0.7625 (t) REVERT: A 912 TYR cc_start: 0.5128 (OUTLIER) cc_final: 0.4465 (p90) REVERT: A 962 THR cc_start: 0.6246 (m) cc_final: 0.5920 (p) outliers start: 41 outliers final: 20 residues processed: 99 average time/residue: 0.8843 time to fit residues: 93.2296 Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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 669 VAL Chi-restraints excluded: chain A residue 762 ILE 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 Chi-restraints excluded: chain A residue 906 TYR 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 33 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 65 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.171557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.149632 restraints weight = 9009.025| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.88 r_work: 0.3885 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5801 Z= 0.194 Angle : 0.575 12.454 7852 Z= 0.292 Chirality : 0.042 0.200 911 Planarity : 0.004 0.040 1008 Dihedral : 5.613 52.333 780 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.95 % Allowed : 20.19 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.32), residues: 699 helix: 1.93 (0.31), residues: 286 sheet: 0.02 (0.43), residues: 148 loop : -0.62 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.004 0.001 HIS A 498 PHE 0.011 0.001 PHE A 497 TYR 0.020 0.001 TYR A 775 ARG 0.002 0.000 ARG A 114 *********************** 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 104 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 66 time to evaluate : 0.599 Fit side-chains REVERT: A 25 ASN cc_start: 0.6312 (t0) cc_final: 0.6090 (m-40) REVERT: A 105 MET cc_start: 0.7491 (mtt) cc_final: 0.7200 (mtm) REVERT: A 136 TYR cc_start: 0.4995 (OUTLIER) cc_final: 0.4604 (p90) REVERT: A 775 TYR cc_start: 0.7652 (t80) cc_final: 0.7439 (t80) REVERT: A 780 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6574 (tt) REVERT: A 855 THR cc_start: 0.7907 (p) cc_final: 0.7650 (t) REVERT: A 895 ASN cc_start: 0.6661 (OUTLIER) cc_final: 0.6158 (m-40) REVERT: A 912 TYR cc_start: 0.5155 (OUTLIER) cc_final: 0.4835 (p90) REVERT: A 962 THR cc_start: 0.6189 (m) cc_final: 0.5877 (p) outliers start: 38 outliers final: 18 residues processed: 95 average time/residue: 1.0061 time to fit residues: 101.2212 Evaluate side-chains 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 228 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 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 762 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.168912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.146819 restraints weight = 9010.352| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.87 r_work: 0.3851 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5801 Z= 0.276 Angle : 0.627 7.762 7852 Z= 0.324 Chirality : 0.044 0.217 911 Planarity : 0.005 0.039 1008 Dihedral : 5.773 55.251 778 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.42 % Allowed : 21.13 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.32), residues: 699 helix: 1.75 (0.31), residues: 286 sheet: -0.03 (0.44), residues: 148 loop : -0.72 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 116 HIS 0.005 0.001 HIS A 498 PHE 0.011 0.002 PHE A 497 TYR 0.020 0.002 TYR A 775 ARG 0.003 0.000 ARG A 367 *********************** 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 103 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 62 time to evaluate : 0.606 Fit side-chains REVERT: A 25 ASN cc_start: 0.6332 (t0) cc_final: 0.6068 (m-40) REVERT: A 105 MET cc_start: 0.7489 (mtt) cc_final: 0.7220 (mtm) REVERT: A 117 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7089 (tt) REVERT: A 120 ASP cc_start: 0.6791 (OUTLIER) cc_final: 0.6405 (t0) REVERT: A 136 TYR cc_start: 0.5078 (OUTLIER) cc_final: 0.4718 (p90) REVERT: A 330 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: A 691 GLN cc_start: 0.7582 (tp40) cc_final: 0.7232 (tp40) REVERT: A 780 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6766 (tt) REVERT: A 855 THR cc_start: 0.7959 (p) cc_final: 0.7675 (t) REVERT: A 884 ARG cc_start: 0.8117 (tpp-160) cc_final: 0.7751 (mpt-90) REVERT: A 895 ASN cc_start: 0.6809 (OUTLIER) cc_final: 0.6252 (m-40) REVERT: A 899 LEU cc_start: 0.6000 (tm) cc_final: 0.5762 (tm) REVERT: A 912 TYR cc_start: 0.5124 (OUTLIER) cc_final: 0.4820 (p90) REVERT: A 962 THR cc_start: 0.6229 (m) cc_final: 0.5912 (p) outliers start: 41 outliers final: 24 residues processed: 94 average time/residue: 0.8421 time to fit residues: 84.6221 Evaluate side-chains 89 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 124 PHE 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 171 VAL Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 330 GLN 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 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 698 GLN 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 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.0170 chunk 63 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.173627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.152149 restraints weight = 8964.663| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.87 r_work: 0.3915 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5801 Z= 0.166 Angle : 0.568 8.183 7852 Z= 0.287 Chirality : 0.043 0.240 911 Planarity : 0.004 0.042 1008 Dihedral : 5.306 48.635 778 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.32 % Allowed : 21.75 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.33), residues: 699 helix: 2.00 (0.32), residues: 287 sheet: -0.03 (0.44), residues: 148 loop : -0.54 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 124 TYR 0.016 0.001 TYR A 775 ARG 0.005 0.000 ARG A 252 *********************** 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 98 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 0.701 Fit side-chains REVERT: A 117 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6826 (tt) REVERT: A 157 PHE cc_start: 0.3999 (OUTLIER) cc_final: 0.3536 (t80) REVERT: A 691 GLN cc_start: 0.7494 (tp40) cc_final: 0.7274 (tp40) REVERT: A 692 LEU cc_start: 0.7957 (tp) cc_final: 0.7755 (tp) REVERT: A 780 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6423 (tt) REVERT: A 855 THR cc_start: 0.7849 (p) cc_final: 0.7568 (t) REVERT: A 895 ASN cc_start: 0.6629 (OUTLIER) cc_final: 0.6050 (m-40) REVERT: A 962 THR cc_start: 0.6167 (m) cc_final: 0.5865 (p) outliers start: 34 outliers final: 13 residues processed: 91 average time/residue: 0.8433 time to fit residues: 81.8956 Evaluate side-chains 73 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU 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 698 GLN 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 895 ASN Chi-restraints excluded: chain A residue 897 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.173373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.151813 restraints weight = 8838.992| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.86 r_work: 0.3907 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5801 Z= 0.183 Angle : 0.595 12.156 7852 Z= 0.301 Chirality : 0.046 0.370 911 Planarity : 0.004 0.040 1008 Dihedral : 5.088 49.415 776 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.07 % Allowed : 23.00 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.32), residues: 699 helix: 1.89 (0.31), residues: 288 sheet: -0.07 (0.44), residues: 151 loop : -0.51 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 116 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 497 TYR 0.021 0.001 TYR A 775 ARG 0.006 0.000 ARG A 252 *********************** 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 89 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.690 Fit side-chains REVERT: A 117 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7125 (tt) REVERT: A 157 PHE cc_start: 0.4014 (OUTLIER) cc_final: 0.3564 (t80) REVERT: A 691 GLN cc_start: 0.7447 (tp40) cc_final: 0.7202 (tp40) REVERT: A 701 LYS cc_start: 0.7063 (tttp) cc_final: 0.6742 (mtpp) REVERT: A 780 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6234 (tt) REVERT: A 855 THR cc_start: 0.7876 (p) cc_final: 0.7580 (t) REVERT: A 895 ASN cc_start: 0.6727 (OUTLIER) cc_final: 0.6229 (m-40) REVERT: A 962 THR cc_start: 0.6168 (m) cc_final: 0.5852 (p) REVERT: A 966 GLN cc_start: 0.6962 (mt0) cc_final: 0.6462 (mm-40) outliers start: 26 outliers final: 17 residues processed: 84 average time/residue: 0.8840 time to fit residues: 79.4305 Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 120 ASP Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 228 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.174513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.153006 restraints weight = 8887.619| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.89 r_work: 0.3923 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2760 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= 0.172 Angle : 0.596 10.493 7852 Z= 0.301 Chirality : 0.045 0.336 911 Planarity : 0.004 0.042 1008 Dihedral : 5.001 47.948 776 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.44 % Allowed : 24.57 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.32), residues: 699 helix: 1.95 (0.31), residues: 288 sheet: 0.04 (0.44), residues: 150 loop : -0.49 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 116 HIS 0.004 0.001 HIS A 498 PHE 0.014 0.001 PHE A 137 TYR 0.009 0.001 TYR A 128 ARG 0.006 0.000 ARG A 252 *********************** 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 79 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.686 Fit side-chains REVERT: A 117 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7087 (tt) REVERT: A 157 PHE cc_start: 0.4033 (OUTLIER) cc_final: 0.3573 (t80) REVERT: A 691 GLN cc_start: 0.7430 (tp40) cc_final: 0.7210 (tp40) REVERT: A 780 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6211 (tt) REVERT: A 855 THR cc_start: 0.7813 (p) cc_final: 0.7539 (t) REVERT: A 884 ARG cc_start: 0.8104 (tpp-160) cc_final: 0.7813 (mpt-90) REVERT: A 895 ASN cc_start: 0.6654 (OUTLIER) cc_final: 0.6144 (m-40) REVERT: A 962 THR cc_start: 0.6164 (m) cc_final: 0.5835 (p) REVERT: A 966 GLN cc_start: 0.6965 (mt0) cc_final: 0.6467 (mm-40) outliers start: 22 outliers final: 12 residues processed: 75 average time/residue: 0.8979 time to fit residues: 72.0147 Evaluate side-chains 73 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 120 ASP Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 217 THR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 chunk 21 optimal weight: 0.1980 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.174908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.153722 restraints weight = 8986.422| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.87 r_work: 0.3932 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5801 Z= 0.165 Angle : 0.587 11.549 7852 Z= 0.296 Chirality : 0.044 0.278 911 Planarity : 0.004 0.041 1008 Dihedral : 4.931 47.647 776 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.82 % Allowed : 25.67 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.32), residues: 699 helix: 2.00 (0.31), residues: 288 sheet: 0.07 (0.44), residues: 151 loop : -0.46 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.015 0.001 PHE A 137 TYR 0.029 0.001 TYR A 775 ARG 0.006 0.000 ARG A 252 ********************** 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 74 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.656 Fit side-chains REVERT: A 157 PHE cc_start: 0.3945 (OUTLIER) cc_final: 0.3546 (t80) REVERT: A 691 GLN cc_start: 0.7381 (tp40) cc_final: 0.7163 (tp40) REVERT: A 780 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6179 (tt) REVERT: A 855 THR cc_start: 0.7781 (p) cc_final: 0.7510 (t) REVERT: A 962 THR cc_start: 0.6148 (m) cc_final: 0.5821 (p) REVERT: A 966 GLN cc_start: 0.6900 (mt0) cc_final: 0.6442 (mm-40) outliers start: 18 outliers final: 13 residues processed: 73 average time/residue: 0.9302 time to fit residues: 72.2756 Evaluate side-chains 68 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 157 PHE Chi-restraints excluded: chain A residue 217 THR 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 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 897 VAL 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 27 optimal weight: 4.9990 chunk 15 optimal weight: 0.0870 chunk 1 optimal weight: 0.2980 chunk 41 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.178359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.157149 restraints weight = 9077.368| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.90 r_work: 0.3976 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3868 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 5801 Z= 0.144 Angle : 0.559 10.472 7852 Z= 0.283 Chirality : 0.043 0.230 911 Planarity : 0.004 0.042 1008 Dihedral : 4.738 48.656 776 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.50 % Allowed : 25.82 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.33), residues: 699 helix: 2.17 (0.31), residues: 288 sheet: -0.02 (0.43), residues: 158 loop : -0.27 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 418 HIS 0.003 0.001 HIS A 498 PHE 0.014 0.001 PHE A 137 TYR 0.026 0.001 TYR A 775 ARG 0.007 0.000 ARG A 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3866.15 seconds wall clock time: 69 minutes 1.44 seconds (4141.44 seconds total)