Starting phenix.real_space_refine on Sun Mar 10 20:03:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/03_2024/7uh3_26504_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/03_2024/7uh3_26504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/03_2024/7uh3_26504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/03_2024/7uh3_26504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/03_2024/7uh3_26504_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/03_2024/7uh3_26504_updated.pdb" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.033 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 1615 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 2032 2.51 5 N 504 2.21 5 O 540 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 GLU 172": "OE1" <-> "OE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "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: 3096 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3096 Number of conformers: 1 Conformer: "" 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 Time building chain proxies: 2.23, per 1000 atoms: 0.72 Number of scatterers: 3096 At special positions: 0 Unit cell: (68.16, 74.124, 75.828, 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 540 8.00 N 504 7.00 C 2032 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: 1.41 Conformation dependent library (CDL) restraints added in 642.5 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 0 sheets defined 80.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 12 through 32 Processing helix chain 'A' and resid 36 through 72 removed outlier: 3.994A pdb=" N LYS A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.662A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.719A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 106 removed outlier: 3.758A pdb=" N ARG A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.982A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 152 through 170 removed outlier: 3.523A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 219 removed outlier: 3.565A pdb=" N TYR A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.506A pdb=" N VAL A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.706A pdb=" N VAL A 225 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 258 through 264 Processing helix chain 'A' and resid 266 through 275 removed outlier: 3.520A pdb=" N LEU A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.807A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 309 removed outlier: 4.143A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 4.214A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 329 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.600A pdb=" N THR A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 370 removed outlier: 4.127A pdb=" N GLY A 359 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 361 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 362 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 364 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 367 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.559A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 415 removed outlier: 4.057A pdb=" N ALA A 391 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 392 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 395 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 396 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 398 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 400 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 413 " --> pdb=" O ALA A 410 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 552 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: 0.78 Time building geometry restraints manager: 1.51 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: 981 1.37 - 1.55: 2142 1.55 - 1.74: 0 1.74 - 1.92: 30 1.92 - 2.10: 1 Bond restraints: 3154 Sorted by residual: bond pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.31e-02 5.83e+03 6.42e+00 bond pdb=" N ASP A 312 " pdb=" CA ASP A 312 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.09e+00 bond pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 2.054 2.102 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" N LEU A 316 " pdb=" CA LEU A 316 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.32e+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 5.05e+00 ... (remaining 3149 not shown) Histogram of bond angle deviations from ideal: 99.00 - 105.45: 74 105.45 - 111.90: 1646 111.90 - 118.35: 843 118.35 - 124.81: 1703 124.81 - 131.26: 34 Bond angle restraints: 4300 Sorted by residual: angle pdb=" N THR A 308 " pdb=" CA THR A 308 " pdb=" C THR A 308 " ideal model delta sigma weight residual 114.31 109.51 4.80 1.29e+00 6.01e-01 1.39e+01 angle pdb=" CB EFC A 385 " pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 101.65 110.15 -8.50 3.00e+00 1.11e-01 8.03e+00 angle pdb=" CA LEU A 244 " pdb=" CB LEU A 244 " pdb=" CG LEU A 244 " ideal model delta sigma weight residual 116.30 126.13 -9.83 3.50e+00 8.16e-02 7.89e+00 angle pdb=" CA LEU A 372 " pdb=" CB LEU A 372 " pdb=" CG LEU A 372 " ideal model delta sigma weight residual 116.30 125.98 -9.68 3.50e+00 8.16e-02 7.65e+00 angle pdb=" CA ASN A 310 " pdb=" C ASN A 310 " pdb=" O ASN A 310 " ideal model delta sigma weight residual 120.98 118.11 2.87 1.08e+00 8.57e-01 7.05e+00 ... (remaining 4295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 1717 14.14 - 28.28: 101 28.28 - 42.42: 27 42.42 - 56.55: 1 56.55 - 70.69: 2 Dihedral angle restraints: 1848 sinusoidal: 669 harmonic: 1179 Sorted by residual: dihedral pdb=" CA THR A 240 " pdb=" C THR A 240 " pdb=" N LEU A 241 " pdb=" CA LEU A 241 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CB LYS A 175 " pdb=" CG LYS A 175 " pdb=" CD LYS A 175 " pdb=" CE LYS A 175 " ideal model delta sinusoidal sigma weight residual -180.00 -139.25 -40.75 3 1.50e+01 4.44e-03 7.27e+00 dihedral pdb=" CA GLU A 9 " pdb=" CB GLU A 9 " pdb=" CG GLU A 9 " pdb=" CD GLU A 9 " ideal model delta sinusoidal sigma weight residual 60.00 100.17 -40.17 3 1.50e+01 4.44e-03 7.15e+00 ... (remaining 1845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 359 0.032 - 0.064: 131 0.064 - 0.096: 30 0.096 - 0.128: 15 0.128 - 0.160: 3 Chirality restraints: 538 Sorted by residual: chirality pdb=" CA ILE A 309 " pdb=" N ILE A 309 " pdb=" C ILE A 309 " pdb=" CB ILE A 309 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA LEU A 316 " pdb=" N LEU A 316 " pdb=" C LEU A 316 " pdb=" CB LEU A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA MET A 311 " pdb=" N MET A 311 " pdb=" C MET A 311 " pdb=" CB MET A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 535 not shown) Planarity restraints: 530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 45 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 172 " -0.005 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" CD GLU A 172 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLU A 172 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU A 172 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 152 " 0.015 5.00e-02 4.00e+02 2.29e-02 8.40e-01 pdb=" N PRO A 153 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.013 5.00e-02 4.00e+02 ... (remaining 527 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 17 2.51 - 3.11: 2485 3.11 - 3.70: 4769 3.70 - 4.30: 6588 4.30 - 4.90: 10640 Nonbonded interactions: 24499 Sorted by model distance: nonbonded pdb=" OD1 ASP A 312 " pdb="NA NA A 504 " model vdw 1.909 2.470 nonbonded pdb=" O ASN A 310 " pdb="NA NA A 503 " model vdw 2.302 2.470 nonbonded pdb=" O SER A 171 " pdb=" NH1 ARG A 177 " model vdw 2.313 2.520 nonbonded pdb=" OE1 GLU A 296 " pdb=" OH TYR A 299 " model vdw 2.315 2.440 nonbonded pdb=" O SER A 349 " pdb="NA NA A 502 " model vdw 2.347 2.470 ... (remaining 24494 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 8.820 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.010 Find NCS groups from input model: 0.080 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:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3154 Z= 0.188 Angle : 0.614 9.828 4300 Z= 0.314 Chirality : 0.040 0.160 538 Planarity : 0.003 0.032 530 Dihedral : 10.051 70.692 1100 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 0.91 (0.39), residues: 410 helix: 1.01 (0.27), residues: 333 sheet: None (None), residues: 0 loop : -0.91 (0.58), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.007 0.001 PHE A 156 TYR 0.009 0.001 TYR A 247 ARG 0.003 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.369 Fit side-chains REVERT: A 125 HIS cc_start: 0.6593 (t-90) cc_final: 0.6131 (OUTLIER) outliers start: 0 outliers final: 2 residues processed: 56 average time/residue: 1.1072 time to fit residues: 64.0117 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.0030 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3154 Z= 0.199 Angle : 0.639 10.589 4300 Z= 0.324 Chirality : 0.041 0.123 538 Planarity : 0.004 0.033 530 Dihedral : 6.767 102.088 446 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.10 % Allowed : 10.84 % Favored : 86.07 % 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: 1.37 (0.39), residues: 410 helix: 1.35 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.83 (0.62), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 32 PHE 0.023 0.002 PHE A 273 TYR 0.016 0.002 TYR A 247 ARG 0.003 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.347 Fit side-chains REVERT: A 125 HIS cc_start: 0.6724 (t-90) cc_final: 0.6264 (t-170) REVERT: A 292 MET cc_start: 0.5615 (tpp) cc_final: 0.5308 (ttp) REVERT: A 296 GLU cc_start: 0.7779 (tp30) cc_final: 0.7433 (tp30) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 0.8121 time to fit residues: 45.7788 Evaluate side-chains 43 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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: 0.8060 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3154 Z= 0.183 Angle : 0.578 10.497 4300 Z= 0.288 Chirality : 0.039 0.133 538 Planarity : 0.004 0.034 530 Dihedral : 4.267 20.380 443 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.72 % Allowed : 13.00 % Favored : 83.28 % 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: 1.59 (0.40), residues: 410 helix: 1.50 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -0.92 (0.66), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 223 PHE 0.021 0.002 PHE A 273 TYR 0.016 0.001 TYR A 299 ARG 0.003 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.354 Fit side-chains REVERT: A 95 PHE cc_start: 0.8372 (t80) cc_final: 0.7842 (t80) REVERT: A 125 HIS cc_start: 0.6738 (t-90) cc_final: 0.6152 (t-170) REVERT: A 269 MET cc_start: 0.8625 (mpt) cc_final: 0.8363 (mpt) REVERT: A 292 MET cc_start: 0.5668 (tpp) cc_final: 0.5284 (ttp) REVERT: A 323 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8690 (m-10) outliers start: 12 outliers final: 4 residues processed: 49 average time/residue: 0.8587 time to fit residues: 43.8024 Evaluate side-chains 47 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.0020 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3154 Z= 0.167 Angle : 0.573 10.236 4300 Z= 0.282 Chirality : 0.039 0.133 538 Planarity : 0.004 0.035 530 Dihedral : 4.225 18.560 443 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.41 % Allowed : 13.93 % Favored : 82.66 % 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: 1.87 (0.41), residues: 410 helix: 1.70 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -0.79 (0.65), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.027 0.002 PHE A 324 TYR 0.016 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.373 Fit side-chains REVERT: A 95 PHE cc_start: 0.8403 (t80) cc_final: 0.7878 (t80) REVERT: A 125 HIS cc_start: 0.6748 (t-90) cc_final: 0.6168 (t-170) REVERT: A 269 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8401 (mpt) REVERT: A 292 MET cc_start: 0.5657 (tpp) cc_final: 0.5359 (ttp) REVERT: A 323 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8713 (m-10) outliers start: 11 outliers final: 4 residues processed: 49 average time/residue: 0.8516 time to fit residues: 43.5387 Evaluate side-chains 46 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 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 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3154 Z= 0.175 Angle : 0.570 10.066 4300 Z= 0.281 Chirality : 0.039 0.135 538 Planarity : 0.004 0.036 530 Dihedral : 4.162 18.109 443 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.33 % Allowed : 16.10 % Favored : 79.57 % 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: 1.93 (0.41), residues: 410 helix: 1.81 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.01 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.023 0.001 PHE A 273 TYR 0.015 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.321 Fit side-chains REVERT: A 95 PHE cc_start: 0.8396 (t80) cc_final: 0.7885 (t80) REVERT: A 125 HIS cc_start: 0.6741 (t-90) cc_final: 0.6173 (t-170) REVERT: A 269 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8408 (mpt) REVERT: A 323 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8762 (m-10) outliers start: 14 outliers final: 6 residues processed: 49 average time/residue: 0.9823 time to fit residues: 49.8396 Evaluate side-chains 45 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 398 THR 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: 5.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 0.0370 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3154 Z= 0.173 Angle : 0.593 9.882 4300 Z= 0.289 Chirality : 0.041 0.303 538 Planarity : 0.004 0.036 530 Dihedral : 4.201 17.544 443 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.02 % Allowed : 17.34 % Favored : 78.64 % 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: 1.84 (0.41), residues: 410 helix: 1.77 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.16 (0.62), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.027 0.001 PHE A 324 TYR 0.015 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.352 Fit side-chains REVERT: A 95 PHE cc_start: 0.8358 (t80) cc_final: 0.7831 (t80) REVERT: A 125 HIS cc_start: 0.6765 (t-90) cc_final: 0.6188 (t-170) outliers start: 13 outliers final: 6 residues processed: 47 average time/residue: 0.9274 time to fit residues: 45.3013 Evaluate side-chains 43 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 398 THR 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: 6.9990 chunk 33 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3154 Z= 0.222 Angle : 0.646 13.194 4300 Z= 0.309 Chirality : 0.042 0.281 538 Planarity : 0.004 0.036 530 Dihedral : 4.213 17.594 443 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.41 % Allowed : 19.20 % Favored : 77.40 % 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: 1.70 (0.41), residues: 410 helix: 1.63 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -1.18 (0.65), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.021 0.002 PHE A 273 TYR 0.016 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.320 Fit side-chains REVERT: A 95 PHE cc_start: 0.8345 (t80) cc_final: 0.7768 (t80) REVERT: A 125 HIS cc_start: 0.6778 (t-90) cc_final: 0.6196 (t-170) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 1.0439 time to fit residues: 48.5842 Evaluate side-chains 43 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 398 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.0770 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 35 optimal weight: 0.0980 chunk 37 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 overall best weight: 0.1876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3154 Z= 0.162 Angle : 0.623 12.847 4300 Z= 0.300 Chirality : 0.041 0.266 538 Planarity : 0.004 0.036 530 Dihedral : 4.243 16.552 443 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.48 % Allowed : 19.81 % Favored : 77.71 % 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: 1.78 (0.40), residues: 410 helix: 1.69 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -0.95 (0.62), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.027 0.001 PHE A 324 TYR 0.013 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8335 (t80) cc_final: 0.7706 (t80) REVERT: A 125 HIS cc_start: 0.6765 (t-90) cc_final: 0.6165 (t-170) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 1.0127 time to fit residues: 47.1942 Evaluate side-chains 43 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 398 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3154 Z= 0.395 Angle : 0.725 11.996 4300 Z= 0.353 Chirality : 0.046 0.334 538 Planarity : 0.004 0.034 530 Dihedral : 4.316 16.994 443 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.79 % Allowed : 19.81 % Favored : 77.40 % 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: 1.54 (0.41), residues: 410 helix: 1.54 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -1.03 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.020 0.002 PHE A 273 TYR 0.020 0.002 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) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.333 Fit side-chains REVERT: A 95 PHE cc_start: 0.8313 (t80) cc_final: 0.7720 (t80) REVERT: A 125 HIS cc_start: 0.6617 (t-90) cc_final: 0.6269 (t-90) REVERT: A 217 MET cc_start: 0.8283 (mtm) cc_final: 0.7979 (ptp) REVERT: A 269 MET cc_start: 0.8558 (mpt) cc_final: 0.8234 (mpp) outliers start: 9 outliers final: 6 residues processed: 41 average time/residue: 0.9910 time to fit residues: 42.1840 Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.8072 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3154 Z= 0.190 Angle : 0.659 12.564 4300 Z= 0.315 Chirality : 0.043 0.317 538 Planarity : 0.004 0.035 530 Dihedral : 4.309 16.323 443 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.79 % Allowed : 20.43 % Favored : 76.78 % 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: 1.50 (0.40), residues: 410 helix: 1.56 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -1.29 (0.62), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 132 PHE 0.027 0.002 PHE A 324 TYR 0.014 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.390 Fit side-chains REVERT: A 95 PHE cc_start: 0.8301 (t80) cc_final: 0.7638 (t80) REVERT: A 125 HIS cc_start: 0.6634 (t-90) cc_final: 0.6228 (t-90) REVERT: A 217 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.8001 (ptp) REVERT: A 323 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8722 (m-10) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 0.9401 time to fit residues: 41.1121 Evaluate side-chains 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 0.0020 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.135026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.086323 restraints weight = 6392.001| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.51 r_work: 0.3129 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3154 Z= 0.181 Angle : 0.647 12.572 4300 Z= 0.307 Chirality : 0.044 0.408 538 Planarity : 0.004 0.034 530 Dihedral : 4.218 16.504 443 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.79 % Allowed : 20.74 % Favored : 76.47 % 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: 1.69 (0.41), residues: 410 helix: 1.66 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.21 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.022 0.002 PHE A 273 TYR 0.014 0.001 TYR A 299 ARG 0.002 0.000 ARG A 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1626.27 seconds wall clock time: 29 minutes 29.43 seconds (1769.43 seconds total)