Starting phenix.real_space_refine on Sun Mar 10 23:21:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugd_26487/03_2024/7ugd_26487_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugd_26487/03_2024/7ugd_26487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugd_26487/03_2024/7ugd_26487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugd_26487/03_2024/7ugd_26487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugd_26487/03_2024/7ugd_26487_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugd_26487/03_2024/7ugd_26487_updated.pdb" } resolution = 2.95 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= 0.036 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 2943 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 2023 2.51 5 N 501 2.21 5 O 535 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3079 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3079 Unusual residues: {' NA': 3} Inner-chain residues flagged as termini: ['pdbres="ASP A 501 "'] Classifications: {'peptide': 415, 'undetermined': 3} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 396, 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: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'EFC:plan-1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 2.11, per 1000 atoms: 0.69 Number of scatterers: 3079 At special positions: 0 Unit cell: (71.568, 74.976, 73.272, 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 535 8.00 N 501 7.00 C 2023 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: 1.26 Conformation dependent library (CDL) restraints added in 633.7 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 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: 21 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 12 through 32 Processing helix chain 'A' and resid 36 through 42 Processing helix chain 'A' and resid 44 through 73 removed outlier: 4.131A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.697A pdb=" N SER A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 107 removed outlier: 3.958A pdb=" N ILE A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 152 through 170 removed outlier: 3.510A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 217 removed outlier: 3.595A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 223 through 245 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 258 through 264 Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.548A pdb=" N LYS A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 302 through 309 removed outlier: 4.493A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 329 removed outlier: 3.520A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.086A pdb=" N VAL A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.835A pdb=" N HIS A 368 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.530A pdb=" N EFC A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 414 removed outlier: 3.854A pdb=" N ARG A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 582 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: 0.87 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 972 1.37 - 1.55: 2133 1.55 - 1.73: 0 1.73 - 1.92: 30 1.92 - 2.10: 1 Bond restraints: 3136 Sorted by residual: bond pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 2.054 2.101 -0.047 2.00e-02 2.50e+03 5.46e+00 bond pdb=" C EFC A 385 " pdb=" O EFC A 385 " ideal model delta sigma weight residual 1.231 1.185 0.046 2.00e-02 2.50e+03 5.40e+00 bond pdb=" C SER A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.79e+00 bond pdb=" C2 EFC A 385 " pdb=" F2 EFC A 385 " ideal model delta sigma weight residual 1.388 1.364 0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" C1 EFC A 385 " pdb=" C2 EFC A 385 " ideal model delta sigma weight residual 1.506 1.526 -0.020 2.00e-02 2.50e+03 1.03e+00 ... (remaining 3131 not shown) Histogram of bond angle deviations from ideal: 100.54 - 106.69: 96 106.69 - 112.83: 1753 112.83 - 118.98: 780 118.98 - 125.13: 1619 125.13 - 131.27: 29 Bond angle restraints: 4277 Sorted by residual: angle pdb=" CB EFC A 385 " pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 101.65 109.08 -7.43 3.00e+00 1.11e-01 6.13e+00 angle pdb=" CA ARG A 77 " pdb=" CB ARG A 77 " pdb=" CG ARG A 77 " ideal model delta sigma weight residual 114.10 118.52 -4.42 2.00e+00 2.50e-01 4.88e+00 angle pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " pdb=" C1 EFC A 385 " ideal model delta sigma weight residual 103.98 109.40 -5.42 3.00e+00 1.11e-01 3.27e+00 angle pdb=" C ARG A 77 " pdb=" CA ARG A 77 " pdb=" CB ARG A 77 " ideal model delta sigma weight residual 110.67 113.31 -2.64 1.52e+00 4.33e-01 3.02e+00 angle pdb=" CA GLY A 293 " pdb=" C GLY A 293 " pdb=" O GLY A 293 " ideal model delta sigma weight residual 118.86 120.54 -1.68 1.07e+00 8.73e-01 2.48e+00 ... (remaining 4272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.65: 1689 14.65 - 29.31: 108 29.31 - 43.96: 34 43.96 - 58.62: 3 58.62 - 73.27: 5 Dihedral angle restraints: 1839 sinusoidal: 661 harmonic: 1178 Sorted by residual: dihedral pdb=" CA GLU A 416 " pdb=" CB GLU A 416 " pdb=" CG GLU A 416 " pdb=" CD GLU A 416 " ideal model delta sinusoidal sigma weight residual 60.00 106.57 -46.57 3 1.50e+01 4.44e-03 8.36e+00 dihedral pdb=" CB MET A 103 " pdb=" CG MET A 103 " pdb=" SD MET A 103 " pdb=" CE MET A 103 " ideal model delta sinusoidal sigma weight residual 60.00 102.38 -42.38 3 1.50e+01 4.44e-03 7.60e+00 dihedral pdb=" N LEU A 339 " pdb=" CA LEU A 339 " pdb=" CB LEU A 339 " pdb=" CG LEU A 339 " ideal model delta sinusoidal sigma weight residual -60.00 -101.32 41.32 3 1.50e+01 4.44e-03 7.39e+00 ... (remaining 1836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 301 0.025 - 0.050: 144 0.050 - 0.074: 71 0.074 - 0.099: 17 0.099 - 0.124: 5 Chirality restraints: 538 Sorted by residual: chirality pdb=" CA VAL A 355 " pdb=" N VAL A 355 " pdb=" C VAL A 355 " pdb=" CB VAL A 355 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA MET A 59 " pdb=" N MET A 59 " pdb=" C MET A 59 " pdb=" CB MET A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA SER A 74 " pdb=" N SER A 74 " pdb=" C SER A 74 " pdb=" CB SER A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 535 not shown) Planarity restraints: 526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 45 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 376 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO A 377 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 77 " 0.005 2.00e-02 2.50e+03 9.71e-03 9.43e-01 pdb=" C ARG A 77 " -0.017 2.00e-02 2.50e+03 pdb=" O ARG A 77 " 0.006 2.00e-02 2.50e+03 pdb=" N LEU A 78 " 0.006 2.00e-02 2.50e+03 ... (remaining 523 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 21 2.58 - 3.16: 2565 3.16 - 3.74: 4691 3.74 - 4.32: 6213 4.32 - 4.90: 10419 Nonbonded interactions: 23909 Sorted by model distance: nonbonded pdb=" O ASN A 310 " pdb="NA NA A 502 " model vdw 2.005 2.470 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.258 2.440 nonbonded pdb=" OE1 GLU A 296 " pdb=" OH TYR A 299 " model vdw 2.308 2.440 nonbonded pdb=" O GLN A 150 " pdb=" OG1 THR A 154 " model vdw 2.372 2.440 nonbonded pdb=" OG SER A 93 " pdb="NA NA A 504 " model vdw 2.372 2.470 ... (remaining 23904 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 8.880 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.350 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:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 3136 Z= 0.148 Angle : 0.450 7.431 4277 Z= 0.221 Chirality : 0.036 0.124 538 Planarity : 0.003 0.027 526 Dihedral : 11.383 73.274 1091 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: 0.34 (0.39), residues: 409 helix: 0.73 (0.28), residues: 317 sheet: None (None), residues: 0 loop : -1.32 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 219 PHE 0.004 0.001 PHE A 273 TYR 0.010 0.001 TYR A 299 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.359 Fit side-chains REVERT: A 174 GLU cc_start: 0.7975 (tp30) cc_final: 0.7490 (tm-30) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 1.1655 time to fit residues: 52.9425 Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3136 Z= 0.216 Angle : 0.521 6.999 4277 Z= 0.268 Chirality : 0.039 0.154 538 Planarity : 0.004 0.035 526 Dihedral : 3.564 18.386 442 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.31 % Allowed : 10.94 % Favored : 88.75 % 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: 1.88 (0.42), residues: 409 helix: 1.86 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.02 (0.65), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.007 0.001 PHE A 46 TYR 0.012 0.001 TYR A 383 ARG 0.005 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.340 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 1.0630 time to fit residues: 44.0709 Evaluate side-chains 36 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.8028 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3136 Z= 0.233 Angle : 0.495 5.757 4277 Z= 0.253 Chirality : 0.037 0.125 538 Planarity : 0.004 0.036 526 Dihedral : 3.436 16.578 442 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.94 % Allowed : 14.38 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.43), residues: 409 helix: 2.11 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -1.10 (0.67), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 215 PHE 0.007 0.001 PHE A 143 TYR 0.013 0.001 TYR A 383 ARG 0.004 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.353 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 39 average time/residue: 1.0807 time to fit residues: 43.6471 Evaluate side-chains 37 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 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: 4.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.0050 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- 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: 0.8050 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3136 Z= 0.278 Angle : 0.512 5.189 4277 Z= 0.262 Chirality : 0.039 0.165 538 Planarity : 0.004 0.037 526 Dihedral : 3.531 17.206 442 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.31 % Allowed : 17.19 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.43), residues: 409 helix: 2.08 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -1.02 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 215 PHE 0.007 0.001 PHE A 143 TYR 0.015 0.001 TYR A 299 ARG 0.006 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.348 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 1.1467 time to fit residues: 43.9514 Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7986 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3136 Z= 0.175 Angle : 0.463 4.894 4277 Z= 0.237 Chirality : 0.037 0.182 538 Planarity : 0.004 0.038 526 Dihedral : 3.377 15.856 442 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.25 % Allowed : 17.81 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.43), residues: 409 helix: 2.29 (0.30), residues: 324 sheet: None (None), residues: 0 loop : -0.94 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.005 0.001 PHE A 156 TYR 0.012 0.001 TYR A 88 ARG 0.003 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.340 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 42 average time/residue: 1.0230 time to fit residues: 44.5860 Evaluate side-chains 36 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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: 0.7980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.7976 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3136 Z= 0.176 Angle : 0.470 4.953 4277 Z= 0.240 Chirality : 0.037 0.174 538 Planarity : 0.004 0.036 526 Dihedral : 3.351 14.822 442 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.19 % Allowed : 17.50 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.43), residues: 409 helix: 2.30 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.17 (0.70), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.006 0.001 PHE A 156 TYR 0.012 0.001 TYR A 88 ARG 0.002 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.337 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 38 average time/residue: 1.0443 time to fit residues: 41.1164 Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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: 0.8012 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3136 Z= 0.227 Angle : 0.497 5.030 4277 Z= 0.254 Chirality : 0.038 0.171 538 Planarity : 0.004 0.036 526 Dihedral : 3.420 15.704 442 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 2.19 % Allowed : 17.19 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.43), residues: 409 helix: 2.28 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -1.18 (0.69), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 215 PHE 0.006 0.001 PHE A 156 TYR 0.013 0.001 TYR A 299 ARG 0.005 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.348 Fit side-chains REVERT: A 291 GLU cc_start: 0.8716 (pm20) cc_final: 0.8338 (pm20) outliers start: 7 outliers final: 1 residues processed: 40 average time/residue: 1.0363 time to fit residues: 42.9631 Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7990 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3136 Z= 0.194 Angle : 0.484 5.121 4277 Z= 0.246 Chirality : 0.037 0.160 538 Planarity : 0.004 0.036 526 Dihedral : 3.391 15.237 442 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.94 % Allowed : 18.44 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.43), residues: 409 helix: 2.30 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.08 (0.70), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 215 PHE 0.006 0.001 PHE A 156 TYR 0.014 0.001 TYR A 88 ARG 0.006 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.352 Fit side-chains REVERT: A 291 GLU cc_start: 0.8720 (pm20) cc_final: 0.8358 (pm20) outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 1.1673 time to fit residues: 44.6693 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 244 LEU 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: 2.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7990 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3136 Z= 0.197 Angle : 0.489 5.365 4277 Z= 0.249 Chirality : 0.037 0.156 538 Planarity : 0.004 0.036 526 Dihedral : 3.392 15.281 442 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.88 % Allowed : 17.50 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.43), residues: 409 helix: 2.31 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.06 (0.69), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 215 PHE 0.005 0.001 PHE A 210 TYR 0.014 0.001 TYR A 88 ARG 0.007 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.394 Fit side-chains REVERT: A 10 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7597 (t80) REVERT: A 291 GLU cc_start: 0.8733 (pm20) cc_final: 0.8354 (pm20) outliers start: 6 outliers final: 2 residues processed: 41 average time/residue: 1.0639 time to fit residues: 45.2069 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7987 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3136 Z= 0.191 Angle : 0.503 7.419 4277 Z= 0.251 Chirality : 0.037 0.139 538 Planarity : 0.004 0.036 526 Dihedral : 3.374 15.112 442 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.94 % Allowed : 18.44 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.43), residues: 409 helix: 2.32 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.99 (0.70), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 215 PHE 0.005 0.001 PHE A 156 TYR 0.014 0.001 TYR A 88 ARG 0.005 0.001 ARG A 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.428 Fit side-chains REVERT: A 10 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7615 (t80) REVERT: A 291 GLU cc_start: 0.8738 (pm20) cc_final: 0.8348 (pm20) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 1.1619 time to fit residues: 45.7466 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.099550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.074444 restraints weight = 6039.755| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.45 r_work: 0.2840 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3136 Z= 0.203 Angle : 0.503 5.628 4277 Z= 0.254 Chirality : 0.037 0.129 538 Planarity : 0.004 0.036 526 Dihedral : 3.412 15.235 442 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.56 % Allowed : 17.81 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.43), residues: 409 helix: 2.33 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -0.95 (0.70), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 215 PHE 0.006 0.001 PHE A 210 TYR 0.014 0.001 TYR A 88 ARG 0.006 0.001 ARG A 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1494.94 seconds wall clock time: 27 minutes 44.10 seconds (1664.10 seconds total)