Starting phenix.real_space_refine on Sun Mar 10 23:40:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugx_26498/03_2024/7ugx_26498_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugx_26498/03_2024/7ugx_26498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugx_26498/03_2024/7ugx_26498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugx_26498/03_2024/7ugx_26498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugx_26498/03_2024/7ugx_26498_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugx_26498/03_2024/7ugx_26498_updated.pdb" } resolution = 2.96 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2999 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians S 16 5.16 5 Na 3 4.78 5 C 2041 2.51 5 N 505 2.21 5 O 542 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 394": "OD1" <-> "OD2" Residue "A ASP 501": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3108 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3108 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 419, 3096 Unusual residues: {' NA': 3} Inner-chain residues flagged as termini: ['pdbres="ASP A 501 "'] Classifications: {'peptide': 416, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 397, None: 3} Not linked: pdbres="ASP A 501 " pdbres=" NA A 502 " Not linked: pdbres=" NA A 502 " pdbres=" NA A 503 " Not linked: pdbres=" NA A 503 " pdbres=" NA A 504 " Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 419, 3096 Unusual residues: {' NA': 3} Inner-chain residues flagged as termini: ['pdbres="ASP A 501 "'] Classifications: {'peptide': 416, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 397, None: 3} Not linked: pdbres="ASP A 501 " pdbres=" NA A 502 " Not linked: pdbres=" NA A 502 " pdbres=" NA A 503 " Not linked: pdbres=" NA A 503 " pdbres=" NA A 504 " Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3140 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 10 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 10 " occ=0.50 Time building chain proxies: 3.79, per 1000 atoms: 1.22 Number of scatterers: 3108 At special positions: 0 Unit cell: (77.532, 74.976, 71.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 Na 3 11.00 F 1 9.00 O 542 8.00 N 505 7.00 C 2041 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 1.2 seconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 3 through 6 No H-bonds generated for 'chain 'A' and resid 3 through 6' Processing helix chain 'A' and resid 12 through 32 Processing helix chain 'A' and resid 36 through 42 removed outlier: 3.656A pdb=" N HIS A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 72 removed outlier: 3.778A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix Processing helix chain 'A' and resid 80 through 106 removed outlier: 4.189A pdb=" N LYS A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.743A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.734A pdb=" N LEU A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 169 removed outlier: 3.550A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 219 removed outlier: 3.529A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 223 through 245 removed outlier: 3.819A pdb=" N GLU A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 254 removed outlier: 3.511A pdb=" N TYR A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.583A pdb=" N LYS A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 307 removed outlier: 3.663A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 312 through 329 removed outlier: 3.630A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.792A pdb=" N ILE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 4.144A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 414 removed outlier: 3.783A pdb=" N GLY A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE A 389 " --> pdb=" O EFC A 385 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 603 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 984 1.37 - 1.55: 2153 1.55 - 1.74: 0 1.74 - 1.92: 30 1.92 - 2.10: 1 Bond restraints: 3168 Sorted by residual: bond pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 2.054 2.101 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C EFC A 385 " pdb=" O EFC A 385 " ideal model delta sigma weight residual 1.231 1.186 0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" N MET A 311 " pdb=" CA MET A 311 " ideal model delta sigma weight residual 1.463 1.489 -0.026 1.31e-02 5.83e+03 3.92e+00 bond pdb=" C2 EFC A 385 " pdb=" F2 EFC A 385 " ideal model delta sigma weight residual 1.388 1.365 0.023 2.00e-02 2.50e+03 1.36e+00 bond pdb=" C1 EFC A 385 " pdb=" C2 EFC A 385 " ideal model delta sigma weight residual 1.506 1.528 -0.022 2.00e-02 2.50e+03 1.18e+00 ... (remaining 3163 not shown) Histogram of bond angle deviations from ideal: 100.56 - 106.69: 96 106.69 - 112.83: 1751 112.83 - 118.96: 801 118.96 - 125.09: 1642 125.09 - 131.22: 32 Bond angle restraints: 4322 Sorted by residual: angle pdb=" CA MET A 311 " pdb=" C MET A 311 " pdb=" O MET A 311 " ideal model delta sigma weight residual 122.37 118.54 3.83 1.15e+00 7.56e-01 1.11e+01 angle pdb=" CB EFC A 385 " pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 101.65 109.47 -7.82 3.00e+00 1.11e-01 6.80e+00 angle pdb=" N MET A 59 " pdb=" CA MET A 59 " pdb=" C MET A 59 " ideal model delta sigma weight residual 109.81 114.19 -4.38 2.21e+00 2.05e-01 3.93e+00 angle pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " pdb=" C1 EFC A 385 " ideal model delta sigma weight residual 103.98 109.75 -5.77 3.00e+00 1.11e-01 3.71e+00 angle pdb=" N ILE A 389 " pdb=" CA ILE A 389 " pdb=" C ILE A 389 " ideal model delta sigma weight residual 109.34 113.31 -3.97 2.08e+00 2.31e-01 3.65e+00 ... (remaining 4317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.09: 1717 15.09 - 30.19: 110 30.19 - 45.28: 23 45.28 - 60.38: 3 60.38 - 75.47: 2 Dihedral angle restraints: 1855 sinusoidal: 671 harmonic: 1184 Sorted by residual: dihedral pdb=" CG ARG A 105 " pdb=" CD ARG A 105 " pdb=" NE ARG A 105 " pdb=" CZ ARG A 105 " ideal model delta sinusoidal sigma weight residual 90.00 130.21 -40.21 2 1.50e+01 4.44e-03 8.89e+00 dihedral pdb=" CB MET A 103 " pdb=" CG MET A 103 " pdb=" SD MET A 103 " pdb=" CE MET A 103 " ideal model delta sinusoidal sigma weight residual 60.00 102.30 -42.30 3 1.50e+01 4.44e-03 7.59e+00 dihedral pdb=" CB MET A 292 " pdb=" CG MET A 292 " pdb=" SD MET A 292 " pdb=" CE MET A 292 " ideal model delta sinusoidal sigma weight residual 60.00 102.23 -42.23 3 1.50e+01 4.44e-03 7.57e+00 ... (remaining 1852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 306 0.023 - 0.046: 118 0.046 - 0.069: 87 0.069 - 0.091: 19 0.091 - 0.114: 9 Chirality restraints: 539 Sorted by residual: chirality pdb=" CA MET A 59 " pdb=" N MET A 59 " pdb=" C MET A 59 " pdb=" CB MET A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" C PRO A 258 " pdb=" CB PRO A 258 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.91e-01 chirality pdb=" CA ILE A 294 " pdb=" N ILE A 294 " pdb=" C ILE A 294 " pdb=" CB ILE A 294 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 536 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A 45 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 394 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" CG ASP A 394 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP A 394 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 394 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 108 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO A 109 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " -0.019 5.00e-02 4.00e+02 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 571 2.77 - 3.30: 3243 3.30 - 3.83: 4859 3.83 - 4.37: 5597 4.37 - 4.90: 9613 Nonbonded interactions: 23883 Sorted by model distance: nonbonded pdb=" O SER A 349 " pdb="NA NA A 503 " model vdw 2.234 2.470 nonbonded pdb=" OG SER A 278 " pdb=" OXT ASP A 501 " model vdw 2.413 2.440 nonbonded pdb=" O THR A 308 " pdb="NA NA A 503 " model vdw 2.425 2.470 nonbonded pdb=" OG1 THR A 398 " pdb=" N ASP A 501 " model vdw 2.425 2.520 nonbonded pdb=" O GLY A 221 " pdb=" N HIS A 223 " model vdw 2.426 2.520 ... (remaining 23878 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 9.060 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.520 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.002 0.047 3168 Z= 0.151 Angle : 0.495 7.822 4322 Z= 0.243 Chirality : 0.035 0.114 539 Planarity : 0.004 0.044 534 Dihedral : 10.608 75.469 1105 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.39), residues: 413 helix: 1.49 (0.27), residues: 324 sheet: None (None), residues: 0 loop : 0.40 (0.69), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.005 0.001 PHE A 210 TYR 0.010 0.001 TYR A 299 ARG 0.005 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.359 Fit side-chains REVERT: A 202 MET cc_start: 0.8380 (mmt) cc_final: 0.8111 (mmt) REVERT: A 245 LEU cc_start: 0.9124 (tp) cc_final: 0.8884 (tt) REVERT: A 257 ASP cc_start: 0.8731 (t0) cc_final: 0.8430 (t0) REVERT: A 267 ASP cc_start: 0.8865 (m-30) cc_final: 0.8637 (m-30) REVERT: A 269 MET cc_start: 0.8906 (mtp) cc_final: 0.8645 (mtm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.9659 time to fit residues: 64.9705 Evaluate side-chains 46 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3168 Z= 0.206 Angle : 0.600 8.517 4322 Z= 0.297 Chirality : 0.039 0.158 539 Planarity : 0.005 0.042 534 Dihedral : 3.485 20.928 446 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.85 % Allowed : 11.11 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.41), residues: 413 helix: 2.17 (0.28), residues: 325 sheet: None (None), residues: 0 loop : 0.37 (0.69), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 215 PHE 0.015 0.001 PHE A 261 TYR 0.021 0.001 TYR A 317 ARG 0.008 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.377 Fit side-chains REVERT: A 245 LEU cc_start: 0.9147 (tp) cc_final: 0.8922 (tt) REVERT: A 269 MET cc_start: 0.8835 (mtp) cc_final: 0.8630 (mtm) REVERT: A 292 MET cc_start: 0.7661 (mmm) cc_final: 0.7417 (mpm) REVERT: A 405 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7124 (m-30) outliers start: 6 outliers final: 1 residues processed: 48 average time/residue: 1.0547 time to fit residues: 52.4915 Evaluate side-chains 48 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 chunk 10 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 overall best weight: 0.6116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3168 Z= 0.181 Angle : 0.547 6.784 4322 Z= 0.270 Chirality : 0.038 0.159 539 Planarity : 0.004 0.045 534 Dihedral : 3.459 16.954 446 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.23 % Allowed : 14.81 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.42), residues: 413 helix: 2.33 (0.28), residues: 325 sheet: None (None), residues: 0 loop : 0.38 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 215 PHE 0.012 0.001 PHE A 261 TYR 0.017 0.001 TYR A 317 ARG 0.007 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.353 Fit side-chains REVERT: A 202 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8274 (mmm) REVERT: A 227 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8493 (mp0) REVERT: A 245 LEU cc_start: 0.9150 (tp) cc_final: 0.8949 (tt) REVERT: A 405 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7105 (m-30) outliers start: 4 outliers final: 0 residues processed: 48 average time/residue: 0.9773 time to fit residues: 48.7310 Evaluate side-chains 46 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.0040 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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: 0.7963 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3168 Z= 0.178 Angle : 0.564 9.067 4322 Z= 0.270 Chirality : 0.038 0.162 539 Planarity : 0.004 0.045 534 Dihedral : 3.411 17.289 446 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.54 % Allowed : 16.05 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.42), residues: 413 helix: 2.22 (0.29), residues: 329 sheet: None (None), residues: 0 loop : 0.51 (0.74), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 219 PHE 0.011 0.001 PHE A 261 TYR 0.015 0.001 TYR A 317 ARG 0.006 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.352 Fit side-chains REVERT: A 292 MET cc_start: 0.7530 (mpm) cc_final: 0.7201 (mpm) REVERT: A 399 MET cc_start: 0.8177 (mmm) cc_final: 0.7469 (tpp) REVERT: A 405 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7171 (m-30) outliers start: 5 outliers final: 0 residues processed: 46 average time/residue: 0.9429 time to fit residues: 45.0782 Evaluate side-chains 44 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.7994 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3168 Z= 0.206 Angle : 0.581 8.853 4322 Z= 0.276 Chirality : 0.039 0.172 539 Planarity : 0.004 0.045 534 Dihedral : 3.419 15.467 446 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.23 % Allowed : 17.90 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.42), residues: 413 helix: 2.23 (0.29), residues: 329 sheet: None (None), residues: 0 loop : 0.54 (0.75), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 219 PHE 0.010 0.001 PHE A 261 TYR 0.013 0.001 TYR A 317 ARG 0.005 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.357 Fit side-chains REVERT: A 292 MET cc_start: 0.7533 (mpm) cc_final: 0.7292 (mpm) REVERT: A 399 MET cc_start: 0.8222 (mmm) cc_final: 0.7831 (tpp) REVERT: A 405 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7435 (t0) outliers start: 4 outliers final: 0 residues processed: 43 average time/residue: 0.9798 time to fit residues: 43.8017 Evaluate side-chains 44 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.7977 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3168 Z= 0.184 Angle : 0.557 10.809 4322 Z= 0.267 Chirality : 0.038 0.169 539 Planarity : 0.004 0.046 534 Dihedral : 3.388 14.886 446 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.54 % Allowed : 17.90 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.43), residues: 413 helix: 2.25 (0.29), residues: 329 sheet: None (None), residues: 0 loop : 0.53 (0.75), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 219 PHE 0.010 0.001 PHE A 261 TYR 0.013 0.001 TYR A 317 ARG 0.004 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.320 Fit side-chains REVERT: A 227 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8369 (mp0) REVERT: A 292 MET cc_start: 0.7604 (mpm) cc_final: 0.7345 (mpm) REVERT: A 399 MET cc_start: 0.8286 (mmm) cc_final: 0.7799 (tpp) REVERT: A 405 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7373 (t0) outliers start: 5 outliers final: 0 residues processed: 47 average time/residue: 1.0174 time to fit residues: 49.5910 Evaluate side-chains 44 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.8041 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3168 Z= 0.250 Angle : 0.589 8.423 4322 Z= 0.285 Chirality : 0.040 0.207 539 Planarity : 0.004 0.045 534 Dihedral : 3.510 16.450 446 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.54 % Allowed : 18.52 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.43), residues: 413 helix: 2.09 (0.29), residues: 334 sheet: None (None), residues: 0 loop : 0.69 (0.80), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 219 PHE 0.009 0.001 PHE A 261 TYR 0.013 0.001 TYR A 299 ARG 0.004 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.360 Fit side-chains REVERT: A 95 PHE cc_start: 0.9081 (t80) cc_final: 0.8876 (t80) REVERT: A 292 MET cc_start: 0.7656 (mpm) cc_final: 0.7387 (mpm) REVERT: A 399 MET cc_start: 0.8363 (mmm) cc_final: 0.8136 (tpp) REVERT: A 405 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7418 (t0) outliers start: 5 outliers final: 0 residues processed: 41 average time/residue: 1.0590 time to fit residues: 45.0490 Evaluate side-chains 41 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8015 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3168 Z= 0.201 Angle : 0.587 11.785 4322 Z= 0.277 Chirality : 0.039 0.194 539 Planarity : 0.004 0.045 534 Dihedral : 3.461 12.771 446 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.62 % Allowed : 19.44 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.43), residues: 413 helix: 2.13 (0.29), residues: 333 sheet: None (None), residues: 0 loop : 0.62 (0.78), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 219 PHE 0.009 0.001 PHE A 261 TYR 0.012 0.001 TYR A 299 ARG 0.004 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.346 Fit side-chains REVERT: A 292 MET cc_start: 0.7648 (mpm) cc_final: 0.7357 (mpm) REVERT: A 399 MET cc_start: 0.8384 (mmm) cc_final: 0.8139 (tpp) REVERT: A 405 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7354 (t0) outliers start: 2 outliers final: 0 residues processed: 43 average time/residue: 0.9919 time to fit residues: 44.3052 Evaluate side-chains 44 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3168 Z= 0.241 Angle : 0.601 11.277 4322 Z= 0.286 Chirality : 0.040 0.197 539 Planarity : 0.004 0.045 534 Dihedral : 3.520 13.944 446 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.31 % Allowed : 20.37 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.43), residues: 413 helix: 2.04 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.82 (0.82), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 219 PHE 0.009 0.001 PHE A 261 TYR 0.013 0.001 TYR A 299 ARG 0.004 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.338 Fit side-chains REVERT: A 292 MET cc_start: 0.7677 (mpm) cc_final: 0.7384 (mpm) REVERT: A 399 MET cc_start: 0.8387 (mmm) cc_final: 0.8156 (tpp) REVERT: A 405 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7373 (t0) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 1.0300 time to fit residues: 45.9212 Evaluate side-chains 43 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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: 0.8002 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3168 Z= 0.178 Angle : 0.578 11.258 4322 Z= 0.272 Chirality : 0.038 0.212 539 Planarity : 0.004 0.045 534 Dihedral : 3.462 14.481 446 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.31 % Allowed : 20.06 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.43), residues: 413 helix: 2.11 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.78 (0.82), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 219 PHE 0.009 0.001 PHE A 261 TYR 0.012 0.001 TYR A 317 ARG 0.005 0.001 ARG A 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.378 Fit side-chains REVERT: A 292 MET cc_start: 0.7640 (mpm) cc_final: 0.7347 (mpm) REVERT: A 405 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7262 (t0) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 1.0367 time to fit residues: 46.2811 Evaluate side-chains 44 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 0.0270 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.118698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.078876 restraints weight = 6000.341| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.46 r_work: 0.3006 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3168 Z= 0.171 Angle : 0.578 11.033 4322 Z= 0.271 Chirality : 0.039 0.210 539 Planarity : 0.004 0.045 534 Dihedral : 3.376 14.234 446 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.31 % Allowed : 20.37 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.43), residues: 413 helix: 2.14 (0.29), residues: 338 sheet: None (None), residues: 0 loop : 0.83 (0.82), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 219 PHE 0.009 0.001 PHE A 261 TYR 0.012 0.001 TYR A 317 ARG 0.005 0.001 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1672.75 seconds wall clock time: 30 minutes 15.44 seconds (1815.44 seconds total)