Starting phenix.real_space_refine on Wed Mar 5 19:37:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ufe_42205/03_2025/8ufe_42205.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufe_42205/03_2025/8ufe_42205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ufe_42205/03_2025/8ufe_42205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufe_42205/03_2025/8ufe_42205.map" model { file = "/net/cci-nas-00/data/ceres_data/8ufe_42205/03_2025/8ufe_42205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufe_42205/03_2025/8ufe_42205.cif" } resolution = 3.68 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= 0.003 sd= 0.144 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 P 1 5.49 5 S 14 5.16 5 C 2260 2.51 5 N 571 2.21 5 O 603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 3449 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3405 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 450} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 2.63, per 1000 atoms: 0.76 Number of scatterers: 3449 At special positions: 0 Unit cell: (79.2, 64.9, 66, 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 14 16.00 P 1 15.00 O 603 8.00 N 571 7.00 C 2260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 421.4 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 826 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 84.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 27 through 38 removed outlier: 4.488A pdb=" N SER A 31 " --> pdb=" O TRP A 27 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 61 removed outlier: 3.884A pdb=" N LEU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Proline residue: A 55 - end of helix Processing helix chain 'A' and resid 64 through 81 removed outlier: 3.865A pdb=" N TYR A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 95 through 115 Processing helix chain 'A' and resid 118 through 147 Proline residue: A 138 - end of helix removed outlier: 3.720A pdb=" N LEU A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 179 Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.683A pdb=" N ALA A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.771A pdb=" N ILE A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 242 removed outlier: 3.734A pdb=" N ALA A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 245 through 267 removed outlier: 3.764A pdb=" N LEU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 281 through 312 Processing helix chain 'A' and resid 316 through 342 removed outlier: 4.288A pdb=" N VAL A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 366 Processing helix chain 'A' and resid 378 through 401 Proline residue: A 395 - end of helix removed outlier: 3.956A pdb=" N ILE A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 443 removed outlier: 4.119A pdb=" N GLY A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix removed outlier: 4.168A pdb=" N VAL A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 456 through 484 removed outlier: 3.969A pdb=" N PHE A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 534 1.30 - 1.43: 838 1.43 - 1.56: 2103 1.56 - 1.69: 11 1.69 - 1.82: 26 Bond restraints: 3512 Sorted by residual: bond pdb=" C30 PTY A 501 " pdb=" O4 PTY A 501 " ideal model delta sigma weight residual 1.331 1.433 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C8 PTY A 501 " pdb=" O7 PTY A 501 " ideal model delta sigma weight residual 1.331 1.432 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C30 PTY A 501 " pdb=" C31 PTY A 501 " ideal model delta sigma weight residual 1.504 1.554 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C31 PTY A 501 " pdb=" C32 PTY A 501 " ideal model delta sigma weight residual 1.520 1.562 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" C11 PTY A 501 " pdb=" C8 PTY A 501 " ideal model delta sigma weight residual 1.504 1.545 -0.041 2.00e-02 2.50e+03 4.22e+00 ... (remaining 3507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 4732 3.39 - 6.78: 48 6.78 - 10.17: 4 10.17 - 13.57: 3 13.57 - 16.96: 1 Bond angle restraints: 4788 Sorted by residual: angle pdb=" O11 PTY A 501 " pdb=" P1 PTY A 501 " pdb=" O14 PTY A 501 " ideal model delta sigma weight residual 92.90 109.86 -16.96 3.00e+00 1.11e-01 3.19e+01 angle pdb=" N ILE A 93 " pdb=" CA ILE A 93 " pdb=" C ILE A 93 " ideal model delta sigma weight residual 111.81 108.56 3.25 8.60e-01 1.35e+00 1.43e+01 angle pdb=" O12 PTY A 501 " pdb=" P1 PTY A 501 " pdb=" O13 PTY A 501 " ideal model delta sigma weight residual 119.61 109.08 10.53 3.00e+00 1.11e-01 1.23e+01 angle pdb=" CA LEU A 201 " pdb=" CB LEU A 201 " pdb=" CG LEU A 201 " ideal model delta sigma weight residual 116.30 128.10 -11.80 3.50e+00 8.16e-02 1.14e+01 angle pdb=" CB MET A 104 " pdb=" CG MET A 104 " pdb=" SD MET A 104 " ideal model delta sigma weight residual 112.70 121.80 -9.10 3.00e+00 1.11e-01 9.20e+00 ... (remaining 4783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 1807 22.84 - 45.67: 190 45.67 - 68.51: 37 68.51 - 91.34: 8 91.34 - 114.18: 1 Dihedral angle restraints: 2043 sinusoidal: 739 harmonic: 1304 Sorted by residual: dihedral pdb=" N1 PTY A 501 " pdb=" C2 PTY A 501 " pdb=" C3 PTY A 501 " pdb=" O11 PTY A 501 " ideal model delta sinusoidal sigma weight residual 65.33 179.51 -114.18 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" CA ALA A 493 " pdb=" C ALA A 493 " pdb=" N HIS A 494 " pdb=" CA HIS A 494 " ideal model delta harmonic sigma weight residual 180.00 -164.14 -15.86 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" C3 PTY A 501 " pdb=" O11 PTY A 501 " pdb=" P1 PTY A 501 " pdb=" O12 PTY A 501 " ideal model delta sinusoidal sigma weight residual -59.77 25.32 -85.09 1 3.00e+01 1.11e-03 9.75e+00 ... (remaining 2040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 377 0.031 - 0.063: 153 0.063 - 0.094: 47 0.094 - 0.125: 16 0.125 - 0.156: 2 Chirality restraints: 595 Sorted by residual: chirality pdb=" CB ILE A 34 " pdb=" CA ILE A 34 " pdb=" CG1 ILE A 34 " pdb=" CG2 ILE A 34 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA SER A 137 " pdb=" N SER A 137 " pdb=" C SER A 137 " pdb=" CB SER A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA PRO A 395 " pdb=" N PRO A 395 " pdb=" C PRO A 395 " pdb=" CB PRO A 395 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 592 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 410 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 411 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 345 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO A 346 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 30 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C LEU A 30 " 0.022 2.00e-02 2.50e+03 pdb=" O LEU A 30 " -0.008 2.00e-02 2.50e+03 pdb=" N SER A 31 " -0.007 2.00e-02 2.50e+03 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 402 2.74 - 3.28: 3645 3.28 - 3.82: 5862 3.82 - 4.36: 6214 4.36 - 4.90: 10917 Nonbonded interactions: 27040 Sorted by model distance: nonbonded pdb=" O SER A 69 " pdb=" OG1 THR A 73 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP A 46 " pdb=" NE2 GLN A 129 " model vdw 2.283 3.120 nonbonded pdb=" O GLY A 94 " pdb=" OG1 THR A 98 " model vdw 2.311 3.040 nonbonded pdb=" O SER A 62 " pdb=" OG SER A 62 " model vdw 2.319 3.040 nonbonded pdb=" O GLY A 151 " pdb=" ND2 ASN A 155 " model vdw 2.378 3.120 ... (remaining 27035 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.450 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.005 0.102 3512 Z= 0.330 Angle : 0.793 16.956 4788 Z= 0.357 Chirality : 0.039 0.156 595 Planarity : 0.004 0.034 592 Dihedral : 19.160 114.175 1217 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.34 % Favored : 94.44 % Rotamer: Outliers : 1.76 % Allowed : 40.59 % Favored : 57.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.92 (0.40), residues: 468 helix: 1.86 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -0.42 (0.64), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 184 HIS 0.000 0.000 HIS A 494 PHE 0.013 0.001 PHE A 327 TYR 0.015 0.001 TYR A 200 ARG 0.007 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.293 Fit side-chains REVERT: A 104 MET cc_start: 0.8194 (mmm) cc_final: 0.7644 (mmt) outliers start: 6 outliers final: 6 residues processed: 82 average time/residue: 0.1103 time to fit residues: 11.8729 Evaluate side-chains 82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 310 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.189181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.170413 restraints weight = 5557.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.174371 restraints weight = 3202.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.177048 restraints weight = 2107.660| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.0507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3512 Z= 0.213 Angle : 0.581 10.991 4788 Z= 0.287 Chirality : 0.038 0.142 595 Planarity : 0.004 0.047 592 Dihedral : 11.719 122.264 545 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.91 % Favored : 94.87 % Rotamer: Outliers : 5.59 % Allowed : 37.94 % Favored : 56.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.96 (0.39), residues: 468 helix: 1.79 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.27 (0.67), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 470 HIS 0.000 0.000 HIS A 369 PHE 0.012 0.001 PHE A 327 TYR 0.006 0.001 TYR A 75 ARG 0.005 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.323 Fit side-chains REVERT: A 104 MET cc_start: 0.8384 (mmm) cc_final: 0.7977 (mmt) REVERT: A 143 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7381 (mt) outliers start: 19 outliers final: 9 residues processed: 94 average time/residue: 0.1228 time to fit residues: 14.6761 Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 434 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.176020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.157129 restraints weight = 5191.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.161226 restraints weight = 2947.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.164062 restraints weight = 1909.731| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3512 Z= 0.234 Angle : 0.600 11.368 4788 Z= 0.296 Chirality : 0.039 0.141 595 Planarity : 0.004 0.045 592 Dihedral : 10.901 102.180 537 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.34 % Favored : 94.44 % Rotamer: Outliers : 6.76 % Allowed : 36.47 % Favored : 56.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.84 (0.39), residues: 468 helix: 1.71 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.35 (0.66), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 470 HIS 0.000 0.000 HIS A 494 PHE 0.012 0.001 PHE A 327 TYR 0.006 0.001 TYR A 466 ARG 0.005 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.366 Fit side-chains REVERT: A 58 GLN cc_start: 0.8019 (tt0) cc_final: 0.7797 (tt0) REVERT: A 75 TYR cc_start: 0.9067 (t80) cc_final: 0.8835 (t80) REVERT: A 104 MET cc_start: 0.8471 (mmm) cc_final: 0.8186 (mmt) REVERT: A 143 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7455 (mt) outliers start: 23 outliers final: 18 residues processed: 96 average time/residue: 0.1037 time to fit residues: 13.2538 Evaluate side-chains 98 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 477 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.176776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.157298 restraints weight = 5212.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.161561 restraints weight = 2863.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.164493 restraints weight = 1831.323| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3512 Z= 0.227 Angle : 0.594 11.615 4788 Z= 0.294 Chirality : 0.039 0.144 595 Planarity : 0.004 0.041 592 Dihedral : 10.587 88.064 537 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 7.65 % Allowed : 35.29 % Favored : 57.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.82 (0.39), residues: 468 helix: 1.74 (0.26), residues: 358 sheet: None (None), residues: 0 loop : -0.48 (0.66), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 470 HIS 0.000 0.000 HIS A 494 PHE 0.012 0.001 PHE A 327 TYR 0.005 0.001 TYR A 466 ARG 0.005 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.360 Fit side-chains REVERT: A 75 TYR cc_start: 0.9019 (t80) cc_final: 0.8795 (t80) REVERT: A 104 MET cc_start: 0.8429 (mmm) cc_final: 0.8096 (mmt) REVERT: A 143 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7391 (mt) outliers start: 26 outliers final: 16 residues processed: 102 average time/residue: 0.1004 time to fit residues: 13.6774 Evaluate side-chains 99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 477 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.0070 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.179121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.160204 restraints weight = 5157.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164515 restraints weight = 2761.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.167477 restraints weight = 1719.752| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3512 Z= 0.223 Angle : 0.596 12.035 4788 Z= 0.296 Chirality : 0.039 0.138 595 Planarity : 0.004 0.040 592 Dihedral : 10.362 78.853 536 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 7.94 % Allowed : 35.59 % Favored : 56.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.71 (0.39), residues: 468 helix: 1.64 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -0.50 (0.66), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 470 HIS 0.000 0.000 HIS A 494 PHE 0.011 0.001 PHE A 327 TYR 0.005 0.001 TYR A 466 ARG 0.006 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.365 Fit side-chains REVERT: A 75 TYR cc_start: 0.9089 (t80) cc_final: 0.8843 (t80) REVERT: A 104 MET cc_start: 0.8350 (mmm) cc_final: 0.8093 (mmt) REVERT: A 143 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7331 (mt) REVERT: A 256 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7075 (mm) REVERT: A 370 ARG cc_start: 0.7352 (ttt-90) cc_final: 0.7117 (ttt-90) outliers start: 27 outliers final: 19 residues processed: 103 average time/residue: 0.0967 time to fit residues: 13.4472 Evaluate side-chains 103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 477 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 12 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.179223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.160496 restraints weight = 5196.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.164810 restraints weight = 2737.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167737 restraints weight = 1688.414| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3512 Z= 0.242 Angle : 0.594 10.183 4788 Z= 0.298 Chirality : 0.039 0.138 595 Planarity : 0.004 0.039 592 Dihedral : 10.250 77.827 536 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 8.53 % Allowed : 34.71 % Favored : 56.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.68 (0.39), residues: 468 helix: 1.59 (0.26), residues: 362 sheet: None (None), residues: 0 loop : -0.42 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 470 HIS 0.000 0.000 HIS A 369 PHE 0.012 0.001 PHE A 161 TYR 0.006 0.001 TYR A 466 ARG 0.005 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.367 Fit side-chains REVERT: A 58 GLN cc_start: 0.8039 (tt0) cc_final: 0.7828 (tt0) REVERT: A 75 TYR cc_start: 0.9074 (t80) cc_final: 0.8833 (t80) REVERT: A 256 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7090 (mm) REVERT: A 370 ARG cc_start: 0.7341 (ttt-90) cc_final: 0.7108 (ttt-90) outliers start: 29 outliers final: 23 residues processed: 105 average time/residue: 0.0993 time to fit residues: 13.9957 Evaluate side-chains 107 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 477 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 38 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.181564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.162797 restraints weight = 5200.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.167121 restraints weight = 2785.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.170118 restraints weight = 1733.871| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3512 Z= 0.200 Angle : 0.628 13.364 4788 Z= 0.304 Chirality : 0.040 0.142 595 Planarity : 0.004 0.037 592 Dihedral : 10.057 77.085 536 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.91 % Favored : 94.87 % Rotamer: Outliers : 5.29 % Allowed : 39.71 % Favored : 55.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.69 (0.39), residues: 468 helix: 1.62 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -0.50 (0.65), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 470 HIS 0.000 0.000 HIS A 494 PHE 0.009 0.001 PHE A 327 TYR 0.006 0.001 TYR A 466 ARG 0.005 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.382 Fit side-chains REVERT: A 75 TYR cc_start: 0.9065 (t80) cc_final: 0.8811 (t80) REVERT: A 256 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7121 (mm) REVERT: A 370 ARG cc_start: 0.7338 (ttt-90) cc_final: 0.7114 (ttt-90) outliers start: 18 outliers final: 14 residues processed: 101 average time/residue: 0.1010 time to fit residues: 13.7034 Evaluate side-chains 99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 434 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 chunk 11 optimal weight: 0.7980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.183489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.164328 restraints weight = 5140.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.168731 restraints weight = 2721.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.171834 restraints weight = 1687.008| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3512 Z= 0.206 Angle : 0.633 13.192 4788 Z= 0.307 Chirality : 0.040 0.143 595 Planarity : 0.004 0.036 592 Dihedral : 9.927 77.717 536 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.34 % Favored : 94.44 % Rotamer: Outliers : 5.59 % Allowed : 39.71 % Favored : 54.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.73 (0.39), residues: 468 helix: 1.63 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -0.45 (0.66), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 470 HIS 0.000 0.000 HIS A 369 PHE 0.009 0.001 PHE A 327 TYR 0.005 0.001 TYR A 466 ARG 0.005 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.393 Fit side-chains REVERT: A 58 GLN cc_start: 0.8043 (tt0) cc_final: 0.7830 (tt0) REVERT: A 75 TYR cc_start: 0.9041 (t80) cc_final: 0.8783 (t80) REVERT: A 256 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7125 (mm) outliers start: 19 outliers final: 16 residues processed: 95 average time/residue: 0.0983 time to fit residues: 12.5098 Evaluate side-chains 99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 434 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.0870 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.185968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167208 restraints weight = 4971.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.171621 restraints weight = 2622.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.174624 restraints weight = 1619.580| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3512 Z= 0.189 Angle : 0.633 13.567 4788 Z= 0.306 Chirality : 0.040 0.165 595 Planarity : 0.004 0.035 592 Dihedral : 9.672 78.516 536 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.56 % Favored : 94.23 % Rotamer: Outliers : 3.53 % Allowed : 42.06 % Favored : 54.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.40), residues: 468 helix: 1.65 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.30 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 470 HIS 0.000 0.000 HIS A 369 PHE 0.008 0.001 PHE A 327 TYR 0.004 0.001 TYR A 466 ARG 0.008 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.525 Fit side-chains REVERT: A 75 TYR cc_start: 0.8953 (t80) cc_final: 0.8710 (t80) REVERT: A 256 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7061 (mm) REVERT: A 284 ARG cc_start: 0.7984 (tpp80) cc_final: 0.7775 (tpt170) outliers start: 12 outliers final: 9 residues processed: 101 average time/residue: 0.1316 time to fit residues: 17.4686 Evaluate side-chains 96 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 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 58 GLN A 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.184214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165322 restraints weight = 5034.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.169621 restraints weight = 2644.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172661 restraints weight = 1644.254| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3512 Z= 0.223 Angle : 0.659 13.775 4788 Z= 0.320 Chirality : 0.041 0.216 595 Planarity : 0.004 0.034 592 Dihedral : 9.471 77.767 536 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.91 % Favored : 94.87 % Rotamer: Outliers : 4.12 % Allowed : 42.35 % Favored : 53.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.69 (0.39), residues: 468 helix: 1.61 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -0.49 (0.65), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 184 HIS 0.000 0.000 HIS A 494 PHE 0.007 0.001 PHE A 292 TYR 0.004 0.001 TYR A 464 ARG 0.007 0.000 ARG A 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.365 Fit side-chains REVERT: A 58 GLN cc_start: 0.8061 (tt0) cc_final: 0.7840 (tt0) REVERT: A 75 TYR cc_start: 0.9028 (t80) cc_final: 0.8712 (t80) REVERT: A 256 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7014 (mm) outliers start: 14 outliers final: 10 residues processed: 99 average time/residue: 0.1059 time to fit residues: 13.7979 Evaluate side-chains 95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.182708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163312 restraints weight = 5164.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167708 restraints weight = 2769.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.170666 restraints weight = 1726.583| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3512 Z= 0.216 Angle : 0.657 14.108 4788 Z= 0.319 Chirality : 0.040 0.212 595 Planarity : 0.004 0.034 592 Dihedral : 9.344 76.823 536 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.91 % Favored : 94.87 % Rotamer: Outliers : 4.12 % Allowed : 42.65 % Favored : 53.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.62 (0.39), residues: 468 helix: 1.57 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -0.53 (0.65), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 184 HIS 0.000 0.000 HIS A 494 PHE 0.007 0.001 PHE A 292 TYR 0.004 0.001 TYR A 466 ARG 0.007 0.000 ARG A 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1271.90 seconds wall clock time: 22 minutes 47.57 seconds (1367.57 seconds total)