Starting phenix.real_space_refine on Tue Feb 11 00:31:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ufe_42205/02_2025/8ufe_42205.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufe_42205/02_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_42205/02_2025/8ufe_42205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufe_42205/02_2025/8ufe_42205.map" model { file = "/net/cci-nas-00/data/ceres_data/8ufe_42205/02_2025/8ufe_42205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufe_42205/02_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-5592/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: 2.86, per 1000 atoms: 0.83 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: 0.95 Conformation dependent library (CDL) restraints added in 469.9 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: 0.29 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: 1.00 Time building geometry restraints manager: 1.11 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.150 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.460 ------------------------------------------------------------------------------- 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 : 0.326 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: 0.1283 time to fit residues: 13.9311 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 : 0.318 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.170413 restraints weight = 5557.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.174390 restraints weight = 3197.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.177015 restraints weight = 2102.107| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 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 : 0.367 Fit side-chains REVERT: A 104 MET cc_start: 0.8382 (mmm) cc_final: 0.7975 (mmt) REVERT: A 143 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7382 (mt) outliers start: 19 outliers final: 9 residues processed: 94 average time/residue: 0.1260 time to fit residues: 15.3463 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 : 0.363 ------------------------------------------------------------------------------- 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: 2.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.173395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.154574 restraints weight = 5223.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158588 restraints weight = 2997.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.161384 restraints weight = 1959.179| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1026 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= 0.285 Angle : 0.627 10.989 4788 Z= 0.312 Chirality : 0.040 0.142 595 Planarity : 0.004 0.044 592 Dihedral : 10.940 99.599 537 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.34 % Favored : 94.44 % Rotamer: Outliers : 7.06 % Allowed : 36.18 % 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: 1.59 (0.39), residues: 468 helix: 1.53 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -0.44 (0.65), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 470 HIS 0.000 0.000 HIS A 494 PHE 0.014 0.002 PHE A 161 TYR 0.007 0.001 TYR A 466 ARG 0.004 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 104 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.356 Fit side-chains REVERT: A 58 GLN cc_start: 0.8063 (tt0) cc_final: 0.7836 (tt0) REVERT: A 75 TYR cc_start: 0.9096 (t80) cc_final: 0.8858 (t80) REVERT: A 104 MET cc_start: 0.8457 (mmm) cc_final: 0.8138 (mmt) REVERT: A 469 LEU cc_start: 0.8657 (mt) cc_final: 0.8390 (tp) outliers start: 24 outliers final: 18 residues processed: 97 average time/residue: 0.1078 time to fit residues: 14.1169 Evaluate side-chains 98 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.177268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.158437 restraints weight = 5205.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.162593 restraints weight = 2920.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.165525 restraints weight = 1883.197| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1068 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= 0.201 Angle : 0.584 11.698 4788 Z= 0.289 Chirality : 0.039 0.140 595 Planarity : 0.004 0.040 592 Dihedral : 10.577 85.231 537 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.34 % Favored : 94.44 % Rotamer: Outliers : 7.35 % Allowed : 36.47 % Favored : 56.18 % 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: 1.78 (0.39), residues: 468 helix: 1.70 (0.26), residues: 358 sheet: None (None), residues: 0 loop : -0.48 (0.65), residues: 110 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 0.010 0.001 PHE A 327 TYR 0.005 0.001 TYR A 466 ARG 0.004 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 107 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.366 Fit side-chains REVERT: A 75 TYR cc_start: 0.9065 (t80) cc_final: 0.8835 (t80) REVERT: A 104 MET cc_start: 0.8412 (mmm) cc_final: 0.8127 (mmt) REVERT: A 143 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7360 (mt) REVERT: A 256 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7089 (mm) outliers start: 25 outliers final: 15 residues processed: 99 average time/residue: 0.1068 time to fit residues: 13.9814 Evaluate side-chains 95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 143 LEU Chi-restraints excluded: chain A residue 160 VAL 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 369 HIS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 441 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 46 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.177004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.158619 restraints weight = 5170.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.162728 restraints weight = 2796.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.165518 restraints weight = 1757.465| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3512 Z= 0.280 Angle : 0.611 9.140 4788 Z= 0.307 Chirality : 0.040 0.139 595 Planarity : 0.004 0.040 592 Dihedral : 10.454 80.840 536 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.34 % Favored : 94.44 % Rotamer: Outliers : 8.82 % Allowed : 35.59 % Favored : 55.59 % 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: 1.53 (0.39), residues: 468 helix: 1.52 (0.26), residues: 360 sheet: None (None), residues: 0 loop : -0.57 (0.65), residues: 108 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 0.006 0.001 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 112 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.390 Fit side-chains REVERT: A 143 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7345 (mt) REVERT: A 256 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7119 (mm) REVERT: A 370 ARG cc_start: 0.7261 (ttt-90) cc_final: 0.7031 (ttt-90) outliers start: 30 outliers final: 22 residues processed: 103 average time/residue: 0.0967 time to fit residues: 13.4563 Evaluate side-chains 103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 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 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 297 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.179184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.160563 restraints weight = 5253.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.164884 restraints weight = 2786.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167822 restraints weight = 1728.591| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3512 Z= 0.202 Angle : 0.601 12.954 4788 Z= 0.298 Chirality : 0.039 0.140 595 Planarity : 0.004 0.036 592 Dihedral : 10.241 76.976 536 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.70 % Favored : 95.09 % Rotamer: Outliers : 7.35 % Allowed : 37.35 % Favored : 55.29 % 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: 1.58 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.53 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.001 0.000 HIS A 494 PHE 0.010 0.001 PHE A 327 TYR 0.010 0.001 TYR A 75 ARG 0.005 0.001 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 114 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.326 Fit side-chains REVERT: A 143 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7319 (mt) REVERT: A 256 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7084 (mm) REVERT: A 370 ARG cc_start: 0.7354 (ttt-90) cc_final: 0.7126 (ttt-90) outliers start: 25 outliers final: 18 residues processed: 106 average time/residue: 0.1072 time to fit residues: 15.1913 Evaluate side-chains 104 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 143 LEU Chi-restraints excluded: chain A residue 160 VAL 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 369 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 441 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4120 r_free = 0.4120 target = 0.181529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.162743 restraints weight = 5176.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.167218 restraints weight = 2766.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.170215 restraints weight = 1714.880| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3512 Z= 0.210 Angle : 0.627 12.909 4788 Z= 0.307 Chirality : 0.040 0.143 595 Planarity : 0.004 0.051 592 Dihedral : 10.119 77.486 536 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.70 % Favored : 95.09 % Rotamer: Outliers : 6.18 % Allowed : 38.53 % Favored : 55.29 % 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: 362 sheet: None (None), residues: 0 loop : -0.55 (0.65), residues: 106 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 0.010 0.001 PHE A 327 TYR 0.009 0.001 TYR A 75 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 108 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.378 Fit side-chains REVERT: A 45 MET cc_start: 0.8493 (ttm) cc_final: 0.8273 (ttt) REVERT: A 58 GLN cc_start: 0.8055 (tt0) cc_final: 0.7851 (tt0) REVERT: A 65 ASP cc_start: 0.7764 (t0) cc_final: 0.7561 (t0) REVERT: A 256 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7055 (mm) REVERT: A 370 ARG cc_start: 0.7384 (ttt-90) cc_final: 0.7170 (ttt-90) outliers start: 21 outliers final: 18 residues processed: 101 average time/residue: 0.1029 time to fit residues: 13.8989 Evaluate side-chains 103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 160 VAL 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 335 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 25 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.180378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.161577 restraints weight = 5186.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.166036 restraints weight = 2767.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.169052 restraints weight = 1710.624| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1485 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= 0.205 Angle : 0.641 13.207 4788 Z= 0.312 Chirality : 0.040 0.136 595 Planarity : 0.004 0.036 592 Dihedral : 9.990 77.795 536 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 5.29 % Allowed : 40.00 % 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: 1.65 (0.39), residues: 468 helix: 1.59 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -0.55 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 470 HIS 0.000 0.000 HIS A 494 PHE 0.009 0.001 PHE A 327 TYR 0.005 0.001 TYR A 466 ARG 0.004 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 103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.365 Fit side-chains REVERT: A 45 MET cc_start: 0.8510 (ttm) cc_final: 0.8247 (ttt) REVERT: A 75 TYR cc_start: 0.8907 (t80) cc_final: 0.8661 (t80) outliers start: 18 outliers final: 17 residues processed: 97 average time/residue: 0.1024 time to fit residues: 13.4516 Evaluate side-chains 98 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 112 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 214 MET 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 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 Chi-restraints excluded: chain A residue 430 VAL 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: 2.9990 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.181347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163194 restraints weight = 5041.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.167353 restraints weight = 2749.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.170172 restraints weight = 1734.566| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1642 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 : 0.641 13.564 4788 Z= 0.310 Chirality : 0.040 0.177 595 Planarity : 0.004 0.036 592 Dihedral : 9.868 77.827 536 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 6.18 % Allowed : 38.82 % 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: 1.71 (0.39), residues: 468 helix: 1.63 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -0.51 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.000 0.000 HIS A 494 PHE 0.009 0.001 PHE A 327 TYR 0.005 0.001 TYR A 466 ARG 0.007 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 103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.343 Fit side-chains REVERT: A 58 GLN cc_start: 0.8065 (tt0) cc_final: 0.7859 (tt0) REVERT: A 75 TYR cc_start: 0.8933 (t80) cc_final: 0.8712 (t80) REVERT: A 256 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7167 (mm) outliers start: 21 outliers final: 17 residues processed: 97 average time/residue: 0.1001 time to fit residues: 12.9061 Evaluate side-chains 98 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 160 VAL Chi-restraints excluded: chain A residue 214 MET 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 357 LEU 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=1.00 ------------------------------------------------------------------------------- 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: 0.9980 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 46 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.183255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.164604 restraints weight = 5063.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168949 restraints weight = 2688.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.171975 restraints weight = 1662.550| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3512 Z= 0.197 Angle : 0.660 14.968 4788 Z= 0.318 Chirality : 0.040 0.209 595 Planarity : 0.004 0.036 592 Dihedral : 9.677 77.230 536 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.70 % Favored : 95.09 % Rotamer: Outliers : 5.00 % Allowed : 40.00 % 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: 1.73 (0.39), residues: 468 helix: 1.67 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -0.58 (0.65), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.000 0.000 HIS A 494 PHE 0.009 0.001 PHE A 327 TYR 0.005 0.001 TYR A 466 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: 17 poor density : 84 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 45 MET cc_start: 0.8528 (ttm) cc_final: 0.8321 (ttt) REVERT: A 75 TYR cc_start: 0.8920 (t80) cc_final: 0.8700 (t80) REVERT: A 256 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7137 (mm) outliers start: 17 outliers final: 16 residues processed: 96 average time/residue: 0.0979 time to fit residues: 12.5654 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 : 0.332 ------------------------------------------------------------------------------- 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 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 357 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 31 optimal weight: 0.0000 chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.0000 chunk 34 optimal weight: 0.0170 overall best weight: 0.3426 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.184826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.165583 restraints weight = 5145.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.170087 restraints weight = 2766.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.173136 restraints weight = 1708.475| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3512 Z= 0.182 Angle : 0.652 14.878 4788 Z= 0.313 Chirality : 0.040 0.209 595 Planarity : 0.005 0.060 592 Dihedral : 9.495 76.566 536 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.70 % Favored : 95.09 % Rotamer: Outliers : 4.12 % Allowed : 40.88 % 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: 1.81 (0.39), residues: 468 helix: 1.74 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -0.61 (0.65), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.000 0.000 HIS A 494 PHE 0.008 0.001 PHE A 327 TYR 0.005 0.001 TYR A 75 ARG 0.007 0.001 ARG A 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1224.38 seconds wall clock time: 22 minutes 45.16 seconds (1365.16 seconds total)