Starting phenix.real_space_refine on Fri Dec 8 00:02:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugd_26487/12_2023/7ugd_26487_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugd_26487/12_2023/7ugd_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_26487/12_2023/7ugd_26487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugd_26487/12_2023/7ugd_26487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugd_26487/12_2023/7ugd_26487_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugd_26487/12_2023/7ugd_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-1.21rc1-5172/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: 2.23, per 1000 atoms: 0.72 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: 1.33 Conformation dependent library (CDL) restraints added in 605.8 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: 0.61 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: 0.73 Time building geometry restraints manager: 1.44 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: 1.770 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: 8.820 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.800 Find NCS groups from input model: 0.090 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:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.830 ------------------------------------------------------------------------------- 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 : 0.344 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 1.1728 time to fit residues: 53.2589 Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4623 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 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: 0.7980 ------------------------------------------------------------------------------- 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: 0.8007 moved from start: 0.2155 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= 0.220 Angle : 0.523 6.919 4277 Z= 0.271 Chirality : 0.039 0.153 538 Planarity : 0.004 0.035 526 Dihedral : 3.540 18.265 442 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.31 % Allowed : 11.56 % Favored : 88.12 % 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: 1.89 (0.42), residues: 409 helix: 1.86 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -1.02 (0.66), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.007 0.001 PHE A 46 TYR 0.013 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 : 0.347 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 1.0537 time to fit residues: 43.7230 Evaluate side-chains 36 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4465 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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: 0.7992 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3136 Z= 0.188 Angle : 0.477 5.629 4277 Z= 0.243 Chirality : 0.037 0.125 538 Planarity : 0.004 0.036 526 Dihedral : 3.375 15.879 442 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.62 % Allowed : 14.38 % Favored : 85.00 % 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: 2.33 (0.43), residues: 409 helix: 2.21 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -1.11 (0.67), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.006 0.001 PHE A 156 TYR 0.012 0.001 TYR A 383 ARG 0.004 0.000 ARG A 395 *********************** 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: 2 poor density : 39 time to evaluate : 0.351 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 1.0439 time to fit residues: 43.3445 Evaluate side-chains 36 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4446 ------------------------------------------------------------------------------- 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: 0.6980 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 0.0010 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3136 Z= 0.174 Angle : 0.463 5.129 4277 Z= 0.236 Chirality : 0.037 0.168 538 Planarity : 0.004 0.037 526 Dihedral : 3.308 15.585 442 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.25 % Allowed : 15.31 % Favored : 83.44 % 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: 2.45 (0.43), residues: 409 helix: 2.28 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.19 (0.69), residues: 82 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 0.011 0.001 TYR A 383 ARG 0.003 0.000 ARG A 395 *********************** 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 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.397 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 40 average time/residue: 1.0793 time to fit residues: 44.6952 Evaluate side-chains 37 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.1121 time to fit residues: 1.5663 ------------------------------------------------------------------------------- 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: 4.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.0170 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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: 0.7980 moved from start: 0.2755 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 : 0.472 4.912 4277 Z= 0.242 Chirality : 0.036 0.124 538 Planarity : 0.004 0.037 526 Dihedral : 3.271 15.213 442 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.56 % Allowed : 16.25 % Favored : 82.19 % 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: 2.35 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.26 (0.67), residues: 83 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 0.011 0.001 TYR A 383 ARG 0.004 0.000 ARG A 77 *********************** 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 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.331 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 40 average time/residue: 1.0057 time to fit residues: 41.7649 Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0807 time to fit residues: 0.5805 ------------------------------------------------------------------------------- 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: 0.6980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.0030 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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: 0.7945 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3136 Z= 0.162 Angle : 0.457 4.963 4277 Z= 0.233 Chirality : 0.036 0.163 538 Planarity : 0.004 0.036 526 Dihedral : 3.259 13.968 442 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 2.70 (0.43), residues: 409 helix: 2.48 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.14 (0.68), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.006 0.001 PHE A 210 TYR 0.012 0.001 TYR A 88 ARG 0.003 0.000 ARG A 77 *********************** 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 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.332 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 1.1047 time to fit residues: 41.2303 Evaluate side-chains 36 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0873 time to fit residues: 0.5868 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.0000 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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: 0.7955 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3136 Z= 0.170 Angle : 0.465 4.963 4277 Z= 0.236 Chirality : 0.036 0.146 538 Planarity : 0.004 0.036 526 Dihedral : 3.237 14.028 442 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 2.70 (0.43), residues: 409 helix: 2.49 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.21 (0.68), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.006 0.001 PHE A 210 TYR 0.012 0.001 TYR A 88 ARG 0.004 0.000 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 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.337 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 39 average time/residue: 1.0348 time to fit residues: 41.9262 Evaluate side-chains 37 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0904 time to fit residues: 0.5910 ------------------------------------------------------------------------------- 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: 2.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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: 0.7956 moved from start: 0.2975 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= 0.177 Angle : 0.471 5.693 4277 Z= 0.238 Chirality : 0.036 0.138 538 Planarity : 0.004 0.036 526 Dihedral : 3.270 14.140 442 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.56 % Allowed : 17.50 % 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: 2.70 (0.43), residues: 409 helix: 2.49 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.22 (0.68), 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 0.013 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 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.337 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 38 average time/residue: 1.0406 time to fit residues: 41.0033 Evaluate side-chains 36 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4721 ------------------------------------------------------------------------------- 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: 0.0370 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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: 0.7968 moved from start: 0.2972 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= 0.188 Angle : 0.534 13.410 4277 Z= 0.254 Chirality : 0.037 0.137 538 Planarity : 0.004 0.035 526 Dihedral : 3.304 14.372 442 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.31 % Allowed : 19.06 % 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: 2.68 (0.43), residues: 409 helix: 2.48 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.22 (0.68), 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 0.013 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 37 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.358 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 1.0487 time to fit residues: 40.2756 Evaluate side-chains 36 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4569 ------------------------------------------------------------------------------- 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: 0.0370 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 33 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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: 0.7941 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3136 Z= 0.165 Angle : 0.472 5.841 4277 Z= 0.239 Chirality : 0.036 0.135 538 Planarity : 0.004 0.035 526 Dihedral : 3.301 13.914 442 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.94 % Allowed : 18.12 % 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: 2.78 (0.44), residues: 409 helix: 2.53 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.07 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.006 0.001 PHE A 210 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 37 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.356 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 35 average time/residue: 1.0531 time to fit residues: 38.2923 Evaluate side-chains 34 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4544 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.096906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.071661 restraints weight = 6002.211| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.47 r_work: 0.2798 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3136 Z= 0.271 Angle : 0.545 7.110 4277 Z= 0.272 Chirality : 0.038 0.126 538 Planarity : 0.004 0.054 526 Dihedral : 3.454 15.937 442 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.31 % Allowed : 18.75 % 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: 2.52 (0.43), residues: 409 helix: 2.32 (0.30), residues: 324 sheet: None (None), residues: 0 loop : -0.98 (0.70), 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 143 TYR 0.014 0.001 TYR A 299 ARG 0.009 0.001 ARG A 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1458.70 seconds wall clock time: 26 minutes 35.23 seconds (1595.23 seconds total)