Starting phenix.real_space_refine on Wed Feb 12 17:37:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e2g_27835/02_2025/8e2g_27835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2g_27835/02_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_27835/02_2025/8e2g_27835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2g_27835/02_2025/8e2g_27835.map" model { file = "/net/cci-nas-00/data/ceres_data/8e2g_27835/02_2025/8e2g_27835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2g_27835/02_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-5592/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: 5.57, per 1000 atoms: 0.69 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: 1.97 Conformation dependent library (CDL) restraints added in 683.8 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: 0.74 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: 3.02 Time building geometry restraints manager: 2.39 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: 11.800 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.190 Set scattering table: 0.000 Process input model: 22.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.160 ------------------------------------------------------------------------------- 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 : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 57 average time/residue: 1.7545 time to fit residues: 105.3227 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 : 0.611 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.173318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.146673 restraints weight = 16811.201| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.05 r_work: 0.3863 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4107 Z= 0.310 Angle : 0.604 5.773 5572 Z= 0.314 Chirality : 0.045 0.151 665 Planarity : 0.005 0.046 697 Dihedral : 6.872 57.834 558 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.42 % Allowed : 19.34 % Favored : 78.24 % 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: -2.09 (0.38), residues: 497 helix: -0.37 (0.45), residues: 129 sheet: -1.40 (0.45), residues: 139 loop : -1.92 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 345 HIS 0.004 0.001 HIS A 222 PHE 0.018 0.002 PHE A 192 TYR 0.008 0.002 TYR A 315 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 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.666 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 54 average time/residue: 1.8110 time to fit residues: 103.0165 Evaluate side-chains 46 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.176444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.152682 restraints weight = 17061.037| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.16 r_work: 0.3899 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4107 Z= 0.178 Angle : 0.540 5.876 5572 Z= 0.274 Chirality : 0.043 0.146 665 Planarity : 0.004 0.045 697 Dihedral : 5.570 58.996 546 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.98 % Allowed : 20.66 % 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: -1.75 (0.38), residues: 497 helix: 0.06 (0.46), residues: 129 sheet: -1.41 (0.44), residues: 141 loop : -1.64 (0.42), residues: 227 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 0.010 0.001 PHE A 192 TYR 0.007 0.001 TYR A 633 ARG 0.003 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 57 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6383 (mp10) outliers start: 9 outliers final: 8 residues processed: 53 average time/residue: 1.8638 time to fit residues: 104.0222 Evaluate side-chains 51 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 846 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: 0.0370 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.177149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.150561 restraints weight = 17099.462| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.06 r_work: 0.3909 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4107 Z= 0.182 Angle : 0.526 5.097 5572 Z= 0.268 Chirality : 0.042 0.141 665 Planarity : 0.004 0.044 697 Dihedral : 5.404 56.908 546 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.42 % Allowed : 20.22 % 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: -1.56 (0.38), residues: 497 helix: 0.40 (0.47), residues: 123 sheet: -1.43 (0.44), residues: 141 loop : -1.49 (0.42), residues: 233 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 0.013 0.001 PHE A 192 TYR 0.007 0.001 TYR A 633 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 58 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 915 LEU cc_start: 0.4793 (tt) cc_final: 0.4491 (tt) outliers start: 11 outliers final: 8 residues processed: 53 average time/residue: 1.7706 time to fit residues: 99.0843 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 : 0.630 ------------------------------------------------------------------------------- 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: 0.7980 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.176922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.150827 restraints weight = 16806.302| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.96 r_work: 0.3913 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1754 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= 0.170 Angle : 0.521 5.318 5572 Z= 0.263 Chirality : 0.042 0.153 665 Planarity : 0.004 0.043 697 Dihedral : 5.281 55.064 546 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.20 % Allowed : 20.22 % Favored : 77.58 % 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: -1.49 (0.39), residues: 497 helix: 0.50 (0.48), residues: 123 sheet: -1.41 (0.44), residues: 143 loop : -1.46 (0.42), residues: 231 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 0.012 0.001 PHE A 192 TYR 0.007 0.001 TYR A 633 ARG 0.004 0.001 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 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 58 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 903 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6518 (tt) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 1.6558 time to fit residues: 92.8135 Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 903 LEU 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: 0.9980 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.177204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.153643 restraints weight = 17066.793| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.07 r_work: 0.3909 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1849 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= 0.178 Angle : 0.518 5.668 5572 Z= 0.263 Chirality : 0.042 0.145 665 Planarity : 0.004 0.045 697 Dihedral : 5.205 53.144 546 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.64 % Allowed : 20.00 % 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: -1.46 (0.39), residues: 497 helix: 0.56 (0.48), residues: 123 sheet: -1.40 (0.45), residues: 143 loop : -1.46 (0.42), residues: 231 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 0.008 0.001 TYR A 315 ARG 0.005 0.001 ARG A 387 *********************** 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: 12 poor density : 47 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 903 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6575 (tt) REVERT: A 920 PHE cc_start: 0.6677 (t80) cc_final: 0.6084 (m-80) outliers start: 12 outliers final: 6 residues processed: 54 average time/residue: 1.6215 time to fit residues: 92.6720 Evaluate side-chains 52 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 903 LEU 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: 0.5980 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.177349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.153890 restraints weight = 17063.174| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.06 r_work: 0.3915 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4107 Z= 0.184 Angle : 0.520 5.893 5572 Z= 0.264 Chirality : 0.043 0.143 665 Planarity : 0.004 0.053 697 Dihedral : 4.955 51.292 544 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % 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: -1.46 (0.39), residues: 497 helix: 0.56 (0.48), residues: 123 sheet: -1.38 (0.45), residues: 143 loop : -1.47 (0.41), residues: 231 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 0.022 0.002 PHE A 391 TYR 0.008 0.001 TYR A 315 ARG 0.006 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 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 903 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6627 (tt) REVERT: A 920 PHE cc_start: 0.6602 (t80) cc_final: 0.6046 (m-80) outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 1.9443 time to fit residues: 108.0652 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 : 0.649 ------------------------------------------------------------------------------- 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 903 LEU 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: 0.7980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.176459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.152981 restraints weight = 17185.800| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.11 r_work: 0.3903 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4107 Z= 0.225 Angle : 0.545 6.343 5572 Z= 0.277 Chirality : 0.043 0.139 665 Planarity : 0.005 0.068 697 Dihedral : 5.029 49.358 544 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % 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: -1.42 (0.38), residues: 497 helix: 0.45 (0.47), residues: 123 sheet: -1.04 (0.49), residues: 126 loop : -1.59 (0.39), residues: 248 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 0.030 0.002 PHE A 391 TYR 0.010 0.001 TYR A 315 ARG 0.009 0.001 ARG A 387 *********************** 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 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 920 PHE cc_start: 0.6625 (t80) cc_final: 0.6062 (m-80) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 1.7728 time to fit residues: 95.7430 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 : 0.695 ------------------------------------------------------------------------------- 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: 2.9990 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.176692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.149737 restraints weight = 17403.452| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.07 r_work: 0.3900 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2128 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= 0.214 Angle : 0.556 7.149 5572 Z= 0.280 Chirality : 0.043 0.137 665 Planarity : 0.005 0.064 697 Dihedral : 4.993 47.741 544 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 1.32 % Allowed : 21.32 % 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: -1.40 (0.38), residues: 497 helix: 0.43 (0.47), residues: 123 sheet: -1.00 (0.49), residues: 126 loop : -1.58 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 345 HIS 0.005 0.001 HIS A 222 PHE 0.028 0.002 PHE A 391 TYR 0.009 0.001 TYR A 315 ARG 0.008 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 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 920 PHE cc_start: 0.6663 (t80) cc_final: 0.6017 (m-80) REVERT: A 942 SER cc_start: 0.8065 (m) cc_final: 0.7855 (m) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 1.7170 time to fit residues: 94.4061 Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 943 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 50 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 0.0060 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.178406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.154906 restraints weight = 16962.949| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.11 r_work: 0.3933 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4107 Z= 0.153 Angle : 0.521 6.563 5572 Z= 0.260 Chirality : 0.042 0.140 665 Planarity : 0.004 0.043 697 Dihedral : 4.774 46.078 544 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.10 % Allowed : 21.54 % 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: -1.33 (0.39), residues: 497 helix: 0.71 (0.48), residues: 123 sheet: -1.30 (0.46), residues: 138 loop : -1.43 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 296 HIS 0.004 0.001 HIS A 222 PHE 0.026 0.002 PHE A 391 TYR 0.007 0.001 TYR A 633 ARG 0.004 0.001 ARG A 387 ********************** 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 58 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 920 PHE cc_start: 0.6569 (t80) cc_final: 0.5959 (m-80) REVERT: A 942 SER cc_start: 0.8038 (m) cc_final: 0.7831 (m) outliers start: 5 outliers final: 4 residues processed: 55 average time/residue: 1.9574 time to fit residues: 113.1747 Evaluate side-chains 52 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 943 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 14 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.178642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.155081 restraints weight = 17244.406| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.16 r_work: 0.3926 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4107 Z= 0.168 Angle : 0.534 7.671 5572 Z= 0.268 Chirality : 0.043 0.135 665 Planarity : 0.004 0.042 697 Dihedral : 4.711 44.119 544 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.88 % Allowed : 23.30 % Favored : 75.82 % 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: -1.38 (0.38), residues: 497 helix: 0.64 (0.48), residues: 123 sheet: -1.33 (0.45), residues: 138 loop : -1.44 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 412 HIS 0.004 0.001 HIS A 398 PHE 0.028 0.002 PHE A 391 TYR 0.008 0.001 TYR A 633 ARG 0.003 0.001 ARG A 625 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6639.72 seconds wall clock time: 117 minutes 13.90 seconds (7033.90 seconds total)