Starting phenix.real_space_refine on Wed Mar 12 18:19:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e2g_27835/03_2025/8e2g_27835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2g_27835/03_2025/8e2g_27835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e2g_27835/03_2025/8e2g_27835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2g_27835/03_2025/8e2g_27835.map" model { file = "/net/cci-nas-00/data/ceres_data/8e2g_27835/03_2025/8e2g_27835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2g_27835/03_2025/8e2g_27835.cif" } resolution = 2.99 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= -0.004 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 2574 2.51 5 N 676 2.21 5 O 756 1.98 5 H 4078 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8110 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 8110 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 28, 'TRANS': 494} Chain breaks: 12 Time building chain proxies: 5.81, per 1000 atoms: 0.72 Number of scatterers: 8110 At special positions: 0 Unit cell: (70.4, 78.32, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 756 8.00 N 676 7.00 C 2574 6.00 H 4078 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 676.3 milliseconds 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 9 sheets defined 24.3% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 225 through 243 Processing helix chain 'A' and resid 247 through 263 removed outlier: 3.818A pdb=" N VAL A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.612A pdb=" N MET A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 removed outlier: 3.520A pdb=" N PHE A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.696A pdb=" N GLN A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 4.181A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 76 removed outlier: 3.880A pdb=" N ALA A 81 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 91 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 104 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 93 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 390 removed outlier: 6.464A pdb=" N ALA A 403 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE A 409 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A 423 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A 411 " --> pdb=" O HIS A 421 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 419 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 504 through 513 removed outlier: 5.553A pdb=" N LEU A 505 " --> pdb=" O THR A 574 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR A 574 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE A 507 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 572 " --> pdb=" O ILE A 507 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS A 566 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A 634 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 716 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 731 through 738 removed outlier: 6.709A pdb=" N GLY A 748 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE A 736 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 746 " --> pdb=" O ILE A 736 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS A 744 " --> pdb=" O PRO A 738 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 902 through 903 removed outlier: 6.909A pdb=" N ILE A 914 " --> pdb=" O LEU A 923 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 940 through 945 removed outlier: 6.668A pdb=" N CYS A 955 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A 943 " --> pdb=" O CYS A 953 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS A 953 " --> pdb=" O VAL A 943 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR A 945 " --> pdb=" O ARG A 951 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ARG A 951 " --> pdb=" O TYR A 945 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 414 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: 2.89 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4058 1.03 - 1.23: 22 1.23 - 1.42: 1641 1.42 - 1.62: 2432 1.62 - 1.81: 32 Bond restraints: 8185 Sorted by residual: bond pdb=" C ALA A 569 " pdb=" N GLY A 570 " ideal model delta sigma weight residual 1.331 1.319 0.012 6.60e-03 2.30e+04 3.19e+00 bond pdb=" CG1 ILE A 231 " pdb=" CD1 ILE A 231 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.31e-01 bond pdb=" CA ALA A 924 " pdb=" C ALA A 924 " ideal model delta sigma weight residual 1.529 1.521 0.008 1.04e-02 9.25e+03 5.74e-01 bond pdb=" CB ASP A 139 " pdb=" CG ASP A 139 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.24e-01 bond pdb=" N GLY A 748 " pdb=" CA GLY A 748 " ideal model delta sigma weight residual 1.456 1.447 0.008 1.16e-02 7.43e+03 4.80e-01 ... (remaining 8180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 14601 1.60 - 3.21: 211 3.21 - 4.81: 26 4.81 - 6.42: 1 6.42 - 8.02: 1 Bond angle restraints: 14840 Sorted by residual: angle pdb=" N ILE A 860 " pdb=" CA ILE A 860 " pdb=" C ILE A 860 " ideal model delta sigma weight residual 112.96 109.50 3.46 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CA LEU A 861 " pdb=" CB LEU A 861 " pdb=" CG LEU A 861 " ideal model delta sigma weight residual 116.30 124.32 -8.02 3.50e+00 8.16e-02 5.25e+00 angle pdb=" CA ILE A 860 " pdb=" C ILE A 860 " pdb=" N LEU A 861 " ideal model delta sigma weight residual 118.65 116.61 2.04 1.07e+00 8.73e-01 3.64e+00 angle pdb=" N GLU A 343 " pdb=" CA GLU A 343 " pdb=" C GLU A 343 " ideal model delta sigma weight residual 110.14 107.38 2.76 1.51e+00 4.39e-01 3.35e+00 angle pdb=" C GLY A 570 " pdb=" N GLY A 571 " pdb=" CA GLY A 571 " ideal model delta sigma weight residual 121.58 120.04 1.54 8.60e-01 1.35e+00 3.20e+00 ... (remaining 14835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 3428 17.42 - 34.84: 296 34.84 - 52.25: 99 52.25 - 69.67: 25 69.67 - 87.09: 10 Dihedral angle restraints: 3858 sinusoidal: 2118 harmonic: 1740 Sorted by residual: dihedral pdb=" CA ILE A 914 " pdb=" C ILE A 914 " pdb=" N LEU A 915 " pdb=" CA LEU A 915 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASP A 430 " pdb=" CB ASP A 430 " pdb=" CG ASP A 430 " pdb=" OD1 ASP A 430 " ideal model delta sinusoidal sigma weight residual -30.00 -83.18 53.18 1 2.00e+01 2.50e-03 9.62e+00 dihedral pdb=" N LYS A 636 " pdb=" CA LYS A 636 " pdb=" CB LYS A 636 " pdb=" CG LYS A 636 " ideal model delta sinusoidal sigma weight residual -60.00 -116.64 56.64 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 342 0.027 - 0.053: 212 0.053 - 0.080: 50 0.080 - 0.106: 37 0.106 - 0.133: 24 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA ILE A 512 " pdb=" N ILE A 512 " pdb=" C ILE A 512 " pdb=" CB ILE A 512 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE A 914 " pdb=" N ILE A 914 " pdb=" C ILE A 914 " pdb=" CB ILE A 914 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A 944 " pdb=" N ILE A 944 " pdb=" C ILE A 944 " pdb=" CB ILE A 944 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 662 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 430 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO A 431 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 627 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 628 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 737 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 738 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " 0.019 5.00e-02 4.00e+02 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 462 2.18 - 2.78: 16811 2.78 - 3.39: 23134 3.39 - 3.99: 30750 3.99 - 4.60: 47132 Nonbonded interactions: 118289 Sorted by model distance: nonbonded pdb=" O PRO A 929 " pdb=" H ASP A 938 " model vdw 1.572 2.450 nonbonded pdb=" OE1 GLN A 151 " pdb=" H GLN A 162 " model vdw 1.588 2.450 nonbonded pdb=" O GLU A 164 " pdb="HH22 ARG A 258 " model vdw 1.594 2.450 nonbonded pdb="HH12 ARG A 289 " pdb=" OD1 ASN A 365 " model vdw 1.598 2.450 nonbonded pdb=" H GLU A 339 " pdb=" OD2 ASP A 342 " model vdw 1.606 2.450 ... (remaining 118284 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: 575.110 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: 0.150 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 612.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4107 Z= 0.211 Angle : 0.603 8.023 5572 Z= 0.319 Chirality : 0.043 0.133 665 Planarity : 0.005 0.042 697 Dihedral : 15.682 87.087 1489 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.42 % Allowed : 19.78 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.77 (0.38), residues: 497 helix: -0.03 (0.48), residues: 120 sheet: -1.38 (0.47), residues: 135 loop : -1.59 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 PHE 0.013 0.002 PHE A 192 TYR 0.007 0.001 TYR A 189 ARG 0.003 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 57 average time/residue: 1.7299 time to fit residues: 104.0422 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 952 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.174385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.150991 restraints weight = 16737.815| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.97 r_work: 0.3893 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4107 Z= 0.238 Angle : 0.571 5.635 5572 Z= 0.295 Chirality : 0.044 0.150 665 Planarity : 0.005 0.045 697 Dihedral : 6.672 58.076 558 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.42 % Allowed : 18.90 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.90 (0.38), residues: 497 helix: -0.17 (0.45), residues: 129 sheet: -1.32 (0.45), residues: 139 loop : -1.80 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 PHE 0.015 0.002 PHE A 192 TYR 0.007 0.001 TYR A 633 ARG 0.004 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6330 (mp10) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 1.7419 time to fit residues: 100.8726 Evaluate side-chains 51 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 961 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.175614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.149236 restraints weight = 17126.893| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.01 r_work: 0.3901 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4107 Z= 0.208 Angle : 0.548 5.940 5572 Z= 0.279 Chirality : 0.043 0.144 665 Planarity : 0.004 0.044 697 Dihedral : 5.575 59.032 546 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.20 % Allowed : 20.00 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.77 (0.38), residues: 497 helix: 0.05 (0.46), residues: 129 sheet: -1.43 (0.44), residues: 141 loop : -1.65 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 PHE 0.012 0.001 PHE A 192 TYR 0.007 0.001 TYR A 633 ARG 0.004 0.001 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6269 (mp10) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 1.6794 time to fit residues: 97.4902 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.176791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.150025 restraints weight = 17126.429| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.09 r_work: 0.3910 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4107 Z= 0.213 Angle : 0.550 5.309 5572 Z= 0.283 Chirality : 0.043 0.141 665 Planarity : 0.004 0.044 697 Dihedral : 5.522 57.001 546 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.44 % Favored : 92.35 % Rotamer: Outliers : 2.42 % Allowed : 19.12 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.66 (0.38), residues: 497 helix: 0.31 (0.47), residues: 123 sheet: -1.48 (0.44), residues: 141 loop : -1.56 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 345 HIS 0.003 0.001 HIS A 222 PHE 0.044 0.002 PHE A 920 TYR 0.007 0.001 TYR A 315 ARG 0.004 0.001 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 53 average time/residue: 1.7171 time to fit residues: 96.1986 Evaluate side-chains 49 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 961 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.173265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.147084 restraints weight = 17011.256| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.98 r_work: 0.3859 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4107 Z= 0.309 Angle : 0.592 5.194 5572 Z= 0.305 Chirality : 0.044 0.136 665 Planarity : 0.005 0.044 697 Dihedral : 5.643 54.490 546 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.42 % Allowed : 19.56 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.81 (0.38), residues: 497 helix: 0.03 (0.46), residues: 123 sheet: -1.28 (0.48), residues: 124 loop : -1.77 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 345 HIS 0.004 0.001 HIS A 222 PHE 0.019 0.002 PHE A 192 TYR 0.012 0.002 TYR A 315 ARG 0.004 0.001 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.685 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 53 average time/residue: 1.6262 time to fit residues: 91.4285 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 0.0060 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.177312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.150462 restraints weight = 17167.779| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.07 r_work: 0.3903 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4107 Z= 0.165 Angle : 0.530 5.481 5572 Z= 0.268 Chirality : 0.043 0.143 665 Planarity : 0.004 0.045 697 Dihedral : 5.349 52.814 546 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.20 % Allowed : 20.00 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.54 (0.38), residues: 497 helix: 0.37 (0.48), residues: 123 sheet: -1.21 (0.48), residues: 126 loop : -1.63 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 PHE 0.010 0.001 PHE A 725 TYR 0.007 0.001 TYR A 633 ARG 0.005 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 2.0162 time to fit residues: 112.2323 Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.176954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.153448 restraints weight = 17203.098| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.03 r_work: 0.3904 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4107 Z= 0.186 Angle : 0.532 5.916 5572 Z= 0.269 Chirality : 0.043 0.133 665 Planarity : 0.004 0.044 697 Dihedral : 5.236 51.079 546 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 1.76 % Allowed : 20.88 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.47 (0.38), residues: 497 helix: 0.46 (0.47), residues: 123 sheet: -1.14 (0.48), residues: 126 loop : -1.61 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 PHE 0.013 0.002 PHE A 424 TYR 0.008 0.001 TYR A 633 ARG 0.004 0.001 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 1.9487 time to fit residues: 111.5835 Evaluate side-chains 50 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.176723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.153309 restraints weight = 17110.090| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.04 r_work: 0.3901 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4107 Z= 0.191 Angle : 0.531 6.692 5572 Z= 0.269 Chirality : 0.043 0.134 665 Planarity : 0.005 0.049 697 Dihedral : 5.200 49.240 546 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 1.76 % Allowed : 21.54 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.38), residues: 497 helix: 0.50 (0.47), residues: 123 sheet: -1.15 (0.48), residues: 126 loop : -1.61 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 412 HIS 0.003 0.001 HIS A 222 PHE 0.013 0.002 PHE A 192 TYR 0.012 0.001 TYR A 315 ARG 0.008 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 1.7719 time to fit residues: 106.4189 Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 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 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.176248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.149829 restraints weight = 17296.492| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.01 r_work: 0.3910 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4107 Z= 0.186 Angle : 0.540 6.684 5572 Z= 0.271 Chirality : 0.043 0.134 665 Planarity : 0.004 0.043 697 Dihedral : 5.150 47.811 546 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 1.54 % Allowed : 21.76 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.40 (0.38), residues: 497 helix: 0.54 (0.47), residues: 123 sheet: -1.05 (0.49), residues: 126 loop : -1.62 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 412 HIS 0.004 0.001 HIS A 222 PHE 0.014 0.002 PHE A 424 TYR 0.011 0.001 TYR A 315 ARG 0.004 0.001 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7936 (p) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 1.9339 time to fit residues: 101.4169 Evaluate side-chains 51 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.177574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.151002 restraints weight = 17082.041| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.04 r_work: 0.3916 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4107 Z= 0.181 Angle : 0.540 6.506 5572 Z= 0.270 Chirality : 0.043 0.135 665 Planarity : 0.005 0.063 697 Dihedral : 5.105 46.441 546 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.54 % Allowed : 21.98 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.38), residues: 497 helix: 0.60 (0.47), residues: 123 sheet: -1.10 (0.49), residues: 121 loop : -1.67 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 412 HIS 0.004 0.001 HIS A 222 PHE 0.013 0.001 PHE A 725 TYR 0.011 0.001 TYR A 315 ARG 0.009 0.001 ARG A 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 SER cc_start: 0.8151 (OUTLIER) cc_final: 0.7942 (p) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 1.8685 time to fit residues: 102.1646 Evaluate side-chains 52 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.177599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.154108 restraints weight = 17343.271| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.11 r_work: 0.3905 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.254 4107 Z= 0.535 Angle : 1.217 59.299 5572 Z= 0.714 Chirality : 0.044 0.201 665 Planarity : 0.007 0.123 697 Dihedral : 5.137 46.469 546 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.32 % Allowed : 22.64 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.44 (0.38), residues: 497 helix: 0.60 (0.47), residues: 123 sheet: -1.10 (0.49), residues: 121 loop : -1.67 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 345 HIS 0.003 0.001 HIS A 222 PHE 0.216 0.008 PHE A 920 TYR 0.011 0.001 TYR A 315 ARG 0.006 0.001 ARG A 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7715.37 seconds wall clock time: 134 minutes 54.46 seconds (8094.46 seconds total)