Starting phenix.real_space_refine on Mon Sep 23 14:47:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufe_42205/09_2024/8ufe_42205.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufe_42205/09_2024/8ufe_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufe_42205/09_2024/8ufe_42205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufe_42205/09_2024/8ufe_42205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufe_42205/09_2024/8ufe_42205.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufe_42205/09_2024/8ufe_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-5461/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: 2.72, per 1000 atoms: 0.79 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 418.8 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: 0.36 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: 1.09 Time building geometry restraints manager: 1.10 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.340 Find NCS groups from input model: 0.050 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:3.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.360 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.366 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: 0.1121 time to fit residues: 12.0387 Evaluate side-chains 82 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 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 fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.356 Fit side-chains REVERT: A 104 MET cc_start: 0.8379 (mmm) cc_final: 0.7941 (mmt) REVERT: A 362 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7687 (mtp) outliers start: 19 outliers final: 9 residues processed: 94 average time/residue: 0.1235 time to fit residues: 14.7835 Evaluate side-chains 86 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 362 MET 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 13 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 0.0570 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 0.0370 chunk 22 optimal weight: 6.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3512 Z= 0.173 Angle : 0.577 11.953 4788 Z= 0.282 Chirality : 0.038 0.139 595 Planarity : 0.004 0.044 592 Dihedral : 10.846 103.255 537 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 4.71 % Allowed : 37.35 % Favored : 57.94 % 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: 1.99 (0.39), residues: 468 helix: 1.84 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.33 (0.66), residues: 110 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 0.010 0.001 PHE A 327 TYR 0.004 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 99 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.395 Fit side-chains REVERT: A 45 MET cc_start: 0.8468 (ttp) cc_final: 0.8265 (ttm) REVERT: A 75 TYR cc_start: 0.8668 (t80) cc_final: 0.8399 (t80) REVERT: A 104 MET cc_start: 0.8396 (mmm) cc_final: 0.8010 (mmt) outliers start: 16 outliers final: 11 residues processed: 94 average time/residue: 0.1117 time to fit residues: 13.8682 Evaluate side-chains 91 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 112 LEU Chi-restraints excluded: chain A residue 139 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 342 VAL Chi-restraints excluded: chain A residue 441 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3512 Z= 0.241 Angle : 0.592 11.171 4788 Z= 0.293 Chirality : 0.039 0.136 595 Planarity : 0.004 0.043 592 Dihedral : 10.520 88.064 537 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.34 % Favored : 94.44 % Rotamer: Outliers : 6.76 % Allowed : 35.29 % Favored : 57.94 % 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: 1.94 (0.39), residues: 468 helix: 1.80 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.36 (0.67), 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 0.012 0.001 PHE A 327 TYR 0.006 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 104 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.361 Fit side-chains REVERT: A 45 MET cc_start: 0.8453 (ttp) cc_final: 0.8200 (ttm) REVERT: A 58 GLN cc_start: 0.8304 (tt0) cc_final: 0.7992 (tt0) REVERT: A 75 TYR cc_start: 0.8755 (t80) cc_final: 0.8471 (t80) REVERT: A 104 MET cc_start: 0.8410 (mmm) cc_final: 0.8029 (mmt) outliers start: 23 outliers final: 16 residues processed: 96 average time/residue: 0.1116 time to fit residues: 14.2040 Evaluate side-chains 100 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3512 Z= 0.247 Angle : 0.600 11.898 4788 Z= 0.297 Chirality : 0.039 0.139 595 Planarity : 0.004 0.041 592 Dihedral : 10.313 78.734 536 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 7.35 % Allowed : 35.59 % 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: 1.73 (0.39), residues: 468 helix: 1.65 (0.26), residues: 358 sheet: None (None), residues: 0 loop : -0.43 (0.65), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 470 HIS 0.001 0.000 HIS A 494 PHE 0.011 0.001 PHE A 327 TYR 0.006 0.001 TYR A 466 ARG 0.004 0.000 ARG A 88 *********************** 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 fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 0.365 Fit side-chains REVERT: A 45 MET cc_start: 0.8470 (ttp) cc_final: 0.8228 (ttm) REVERT: A 75 TYR cc_start: 0.8757 (t80) cc_final: 0.8493 (t80) REVERT: A 104 MET cc_start: 0.8408 (mmm) cc_final: 0.8053 (mmt) REVERT: A 256 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7325 (mm) outliers start: 25 outliers final: 19 residues processed: 102 average time/residue: 0.1041 time to fit residues: 14.1323 Evaluate side-chains 105 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 107 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 160 VAL Chi-restraints excluded: chain A residue 209 THR 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 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 11 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3512 Z= 0.273 Angle : 0.628 9.999 4788 Z= 0.310 Chirality : 0.040 0.138 595 Planarity : 0.004 0.040 592 Dihedral : 10.297 77.027 536 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 : 7.65 % Allowed : 35.59 % 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: 1.62 (0.39), residues: 468 helix: 1.56 (0.26), residues: 361 sheet: None (None), residues: 0 loop : -0.45 (0.65), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 27 HIS 0.000 0.000 HIS A 369 PHE 0.013 0.001 PHE A 161 TYR 0.007 0.001 TYR A 466 ARG 0.006 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 113 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 0.373 Fit side-chains REVERT: A 58 GLN cc_start: 0.8297 (tt0) cc_final: 0.7992 (tt0) REVERT: A 75 TYR cc_start: 0.8691 (t80) cc_final: 0.8427 (t80) REVERT: A 104 MET cc_start: 0.8434 (mmm) cc_final: 0.8106 (mmt) REVERT: A 256 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7420 (mm) REVERT: A 401 ILE cc_start: 0.8761 (pt) cc_final: 0.8553 (pt) outliers start: 26 outliers final: 20 residues processed: 102 average time/residue: 0.0990 time to fit residues: 13.5074 Evaluate side-chains 105 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 107 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 397 THR Chi-restraints excluded: chain A residue 434 VAL 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 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1530 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= 0.201 Angle : 0.631 13.387 4788 Z= 0.305 Chirality : 0.040 0.138 595 Planarity : 0.004 0.037 592 Dihedral : 10.085 76.258 536 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 5.00 % Allowed : 38.24 % 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: 1.76 (0.39), residues: 468 helix: 1.67 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -0.48 (0.65), residues: 107 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 0.009 0.001 PHE A 327 TYR 0.005 0.001 TYR A 466 ARG 0.005 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 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 104 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.355 Fit side-chains REVERT: A 75 TYR cc_start: 0.8680 (t80) cc_final: 0.8400 (t80) outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 0.0995 time to fit residues: 13.1826 Evaluate side-chains 96 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 342 VAL Chi-restraints excluded: chain A residue 357 LEU 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 4 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.0040 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1559 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= 0.205 Angle : 0.628 12.493 4788 Z= 0.304 Chirality : 0.040 0.151 595 Planarity : 0.004 0.036 592 Dihedral : 9.927 76.781 536 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 5.29 % Allowed : 40.29 % 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: 1.78 (0.39), residues: 468 helix: 1.68 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -0.47 (0.66), 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 0.009 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 107 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.342 Fit side-chains REVERT: A 58 GLN cc_start: 0.8273 (tt0) cc_final: 0.7953 (tt0) REVERT: A 75 TYR cc_start: 0.8661 (t80) cc_final: 0.8379 (t80) outliers start: 18 outliers final: 16 residues processed: 100 average time/residue: 0.1016 time to fit residues: 13.5193 Evaluate side-chains 101 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 160 VAL 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 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 434 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3512 Z= 0.224 Angle : 0.647 11.622 4788 Z= 0.316 Chirality : 0.041 0.178 595 Planarity : 0.004 0.035 592 Dihedral : 9.747 76.094 536 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 6.47 % Allowed : 39.41 % Favored : 54.12 % 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: 1.68 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -0.45 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.000 0.000 HIS A 369 PHE 0.008 0.001 PHE A 292 TYR 0.004 0.001 TYR A 466 ARG 0.005 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 109 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.336 Fit side-chains REVERT: A 75 TYR cc_start: 0.8656 (t80) cc_final: 0.8382 (t80) REVERT: A 256 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7356 (mm) outliers start: 22 outliers final: 20 residues processed: 103 average time/residue: 0.0981 time to fit residues: 13.6029 Evaluate side-chains 105 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 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 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 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 22 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1725 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= 0.211 Angle : 0.655 13.731 4788 Z= 0.316 Chirality : 0.040 0.208 595 Planarity : 0.004 0.034 592 Dihedral : 9.594 76.394 536 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.91 % Favored : 94.87 % Rotamer: Outliers : 5.88 % Allowed : 40.00 % Favored : 54.12 % 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: 1.75 (0.39), residues: 468 helix: 1.66 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -0.46 (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 494 PHE 0.007 0.001 PHE A 292 TYR 0.005 0.001 TYR A 466 ARG 0.003 0.000 ARG A 88 ********************** 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 108 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.384 Fit side-chains REVERT: A 58 GLN cc_start: 0.8279 (tt0) cc_final: 0.7954 (tt0) REVERT: A 75 TYR cc_start: 0.8645 (t80) cc_final: 0.8367 (t80) REVERT: A 256 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7343 (mm) REVERT: A 370 ARG cc_start: 0.8376 (tpp80) cc_final: 0.8139 (tpp80) outliers start: 20 outliers final: 19 residues processed: 103 average time/residue: 0.1027 time to fit residues: 14.1297 Evaluate side-chains 107 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 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 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 6 optimal weight: 6.9990 chunk 32 optimal weight: 0.0060 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.183659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.164912 restraints weight = 5058.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.169284 restraints weight = 2635.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.172259 restraints weight = 1617.247| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1810 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= 0.204 Angle : 0.647 13.695 4788 Z= 0.313 Chirality : 0.040 0.214 595 Planarity : 0.004 0.034 592 Dihedral : 9.434 77.098 536 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.34 % Favored : 94.44 % Rotamer: Outliers : 6.18 % Allowed : 39.71 % Favored : 54.12 % 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: 1.75 (0.39), residues: 468 helix: 1.67 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -0.50 (0.65), residues: 107 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 0.007 0.001 PHE A 292 TYR 0.004 0.001 TYR A 466 ARG 0.003 0.000 ARG A 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1008.08 seconds wall clock time: 18 minutes 52.86 seconds (1132.86 seconds total)