Starting phenix.real_space_refine on Thu Dec 7 21:01:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/12_2023/7uh3_26504_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/12_2023/7uh3_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_26504/12_2023/7uh3_26504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/12_2023/7uh3_26504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/12_2023/7uh3_26504_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/12_2023/7uh3_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-1.21rc1-5172/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: 2.16, per 1000 atoms: 0.70 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: 1.30 Conformation dependent library (CDL) restraints added in 578.5 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: 0.66 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: 0.86 Time building geometry restraints manager: 1.42 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: 1.900 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: 0.010 Extract box with map and model: 8.730 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.310 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.080 ------------------------------------------------------------------------------- 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 : 0.354 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 56 average time/residue: 1.0608 time to fit residues: 61.3129 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.8369 time to fit residues: 2.3055 ------------------------------------------------------------------------------- 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: 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: 8.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3154 Z= 0.217 Angle : 0.651 10.675 4300 Z= 0.333 Chirality : 0.041 0.120 538 Planarity : 0.005 0.033 530 Dihedral : 4.488 23.960 443 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.41 % Allowed : 10.53 % 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: 1.50 (0.39), residues: 410 helix: 1.45 (0.27), residues: 332 sheet: None (None), residues: 0 loop : -0.87 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 32 PHE 0.024 0.003 PHE A 273 TYR 0.015 0.002 TYR A 247 ARG 0.003 0.001 ARG A 105 *********************** 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 56 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.350 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 52 average time/residue: 0.8325 time to fit residues: 45.1036 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0318 time to fit residues: 0.5012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 0.0770 chunk 37 optimal weight: 0.0170 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3154 Z= 0.152 Angle : 0.573 10.480 4300 Z= 0.287 Chirality : 0.039 0.126 538 Planarity : 0.004 0.035 530 Dihedral : 4.343 20.766 443 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.72 % Allowed : 11.46 % Favored : 84.83 % 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: 1.48 (0.40), residues: 410 helix: 1.51 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.27 (0.64), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.025 0.002 PHE A 273 TYR 0.017 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 : 0.333 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 49 average time/residue: 0.8729 time to fit residues: 44.5327 Evaluate side-chains 46 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.5167 time to fit residues: 1.5490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.3003 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= 0.168 Angle : 0.574 10.278 4300 Z= 0.284 Chirality : 0.039 0.128 538 Planarity : 0.004 0.035 530 Dihedral : 4.242 18.687 443 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.10 % Allowed : 14.86 % Favored : 82.04 % 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: 1.75 (0.41), residues: 410 helix: 1.63 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -0.92 (0.64), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 264 PHE 0.025 0.002 PHE A 324 TYR 0.015 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 52 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.381 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 49 average time/residue: 0.8016 time to fit residues: 41.0214 Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.319 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0311 time to fit residues: 0.4700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3154 Z= 0.172 Angle : 0.565 9.882 4300 Z= 0.280 Chirality : 0.039 0.135 538 Planarity : 0.004 0.036 530 Dihedral : 4.159 18.249 443 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.02 % Allowed : 16.10 % Favored : 79.88 % 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: 1.80 (0.41), residues: 410 helix: 1.67 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -0.88 (0.65), residues: 76 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 0.013 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 55 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.342 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 49 average time/residue: 0.8865 time to fit residues: 45.1878 Evaluate side-chains 43 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.6279 time to fit residues: 1.7687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 0.0010 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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: 0.8035 moved from start: 0.3381 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= 0.178 Angle : 0.585 9.831 4300 Z= 0.287 Chirality : 0.041 0.287 538 Planarity : 0.004 0.036 530 Dihedral : 4.145 17.969 443 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.41 % Allowed : 17.03 % 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: 1.69 (0.41), residues: 410 helix: 1.63 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.02 (0.61), residues: 77 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 0.014 0.001 TYR A 299 ARG 0.001 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 55 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.307 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.9103 time to fit residues: 47.2999 Evaluate side-chains 45 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.4498 time to fit residues: 1.8998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8050 moved from start: 0.3496 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= 0.197 Angle : 0.596 12.800 4300 Z= 0.291 Chirality : 0.040 0.228 538 Planarity : 0.004 0.036 530 Dihedral : 4.149 17.739 443 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.72 % Allowed : 19.20 % Favored : 77.09 % 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: 1.67 (0.41), residues: 410 helix: 1.57 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -0.95 (0.62), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.020 0.002 PHE A 273 TYR 0.014 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 54 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.345 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 46 average time/residue: 0.9509 time to fit residues: 45.3858 Evaluate side-chains 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0571 time to fit residues: 0.6120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 35 optimal weight: 0.0870 chunk 37 optimal weight: 0.0040 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 overall best weight: 0.5172 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3154 Z= 0.171 Angle : 0.641 12.740 4300 Z= 0.304 Chirality : 0.043 0.339 538 Planarity : 0.004 0.037 530 Dihedral : 4.151 16.976 443 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.48 % Allowed : 19.50 % Favored : 78.02 % 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: 1.65 (0.40), residues: 410 helix: 1.60 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.07 (0.58), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.030 0.002 PHE A 324 TYR 0.014 0.001 TYR A 299 ARG 0.003 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 51 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.344 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 46 average time/residue: 0.9529 time to fit residues: 45.4895 Evaluate side-chains 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.9793 time to fit residues: 1.4472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.3680 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= 0.207 Angle : 0.666 12.491 4300 Z= 0.315 Chirality : 0.044 0.360 538 Planarity : 0.004 0.036 530 Dihedral : 4.114 16.406 443 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.17 % Allowed : 20.43 % 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: 1.58 (0.41), residues: 410 helix: 1.58 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.16 (0.60), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.020 0.002 PHE A 273 TYR 0.015 0.001 TYR A 299 ARG 0.002 0.000 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 51 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.348 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.9518 time to fit residues: 46.4626 Evaluate side-chains 43 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0829 time to fit residues: 0.5736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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: 0.8034 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3154 Z= 0.192 Angle : 0.673 12.573 4300 Z= 0.317 Chirality : 0.045 0.383 538 Planarity : 0.004 0.036 530 Dihedral : 4.106 16.511 443 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.86 % Allowed : 21.05 % Favored : 77.09 % 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: 1.60 (0.40), residues: 410 helix: 1.59 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.15 (0.59), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.025 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 47 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.351 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 1.0078 time to fit residues: 46.0211 Evaluate side-chains 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0356 time to fit residues: 0.5460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.0370 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6016 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.137271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.088118 restraints weight = 6342.156| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.51 r_work: 0.3212 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3857 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= 0.183 Angle : 0.669 12.518 4300 Z= 0.314 Chirality : 0.044 0.371 538 Planarity : 0.004 0.036 530 Dihedral : 4.087 16.492 443 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.24 % Allowed : 22.60 % Favored : 76.16 % 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 (0.41), residues: 410 helix: 1.57 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.09 (0.62), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.022 0.002 PHE A 95 TYR 0.014 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1601.40 seconds wall clock time: 29 minutes 7.53 seconds (1747.53 seconds total)