Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:54:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/11_2022/6z3t_11064_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/11_2022/6z3t_11064.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/11_2022/6z3t_11064_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/11_2022/6z3t_11064_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/11_2022/6z3t_11064_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/11_2022/6z3t_11064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/11_2022/6z3t_11064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/11_2022/6z3t_11064_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/11_2022/6z3t_11064_updated.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3608 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2977 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 4 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 478 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'Q6B': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.57, per 1000 atoms: 0.71 Number of scatterers: 3608 At special positions: 0 Unit cell: (84.706, 82.64, 85.739, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 621 8.00 N 581 7.00 C 2384 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: 1.42 Conformation dependent library (CDL) restraints added in 681.0 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 858 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 2 sheets defined 65.3% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 28 through 43 removed outlier: 3.736A pdb=" N VAL A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 110 through 132 removed outlier: 4.024A pdb=" N LYS A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 167 removed outlier: 4.222A pdb=" N VAL A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 removed outlier: 4.045A pdb=" N ILE A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 192 " --> pdb=" O CYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.876A pdb=" N ARG A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.559A pdb=" N ILE A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 312 removed outlier: 3.772A pdb=" N ILE A 291 " --> pdb=" O ASN A 288 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU A 293 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASN A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 301 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL A 303 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 310 " --> pdb=" O MET A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 358 through 380 removed outlier: 3.529A pdb=" N VAL A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N CYS A 372 " --> pdb=" O MET A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 removed outlier: 4.176A pdb=" N LYS A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 414 No H-bonds generated for 'chain 'A' and resid 411 through 414' Processing helix chain 'A' and resid 417 through 435 removed outlier: 3.836A pdb=" N GLY A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 463 removed outlier: 5.095A pdb=" N VAL A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 22 Processing helix chain 'B' and resid 32 through 64 removed outlier: 4.098A pdb=" N PHE B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY B 51 " --> pdb=" O MET B 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 30 through 47 removed outlier: 4.223A pdb=" N UNK C 34 " --> pdb=" O UNK C 30 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 262 through 265 Processing sheet with id= B, first strand: chain 'A' and resid 267 through 269 removed outlier: 3.791A pdb=" N VAL A 400 " --> pdb=" O LYS A 268 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 480 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: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1085 1.34 - 1.46: 873 1.46 - 1.58: 1674 1.58 - 1.71: 10 1.71 - 1.83: 37 Bond restraints: 3679 Sorted by residual: bond pdb=" C06 Q6B A 501 " pdb=" C07 Q6B A 501 " ideal model delta sigma weight residual 1.573 1.410 0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" CA ILE A 281 " pdb=" C ILE A 281 " ideal model delta sigma weight residual 1.524 1.613 -0.089 1.11e-02 8.12e+03 6.37e+01 bond pdb=" CA GLU A 406 " pdb=" C GLU A 406 " ideal model delta sigma weight residual 1.522 1.434 0.089 1.38e-02 5.25e+03 4.12e+01 bond pdb=" C04 Q6B A 501 " pdb=" C40 Q6B A 501 " ideal model delta sigma weight residual 1.526 1.651 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C09 Q6B A 501 " pdb=" C10 Q6B A 501 " ideal model delta sigma weight residual 1.501 1.617 -0.116 2.00e-02 2.50e+03 3.39e+01 ... (remaining 3674 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.60: 78 105.60 - 112.70: 1888 112.70 - 119.81: 1341 119.81 - 126.92: 1636 126.92 - 134.02: 34 Bond angle restraints: 4977 Sorted by residual: angle pdb=" C22 Q6B A 501 " pdb=" C23 Q6B A 501 " pdb=" C24 Q6B A 501 " ideal model delta sigma weight residual 85.89 125.77 -39.88 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C43 Q6B A 501 " pdb=" C44 Q6B A 501 " pdb=" C45 Q6B A 501 " ideal model delta sigma weight residual 85.87 124.06 -38.19 3.00e+00 1.11e-01 1.62e+02 angle pdb=" C21 Q6B A 501 " pdb=" C22 Q6B A 501 " pdb=" C32 Q6B A 501 " ideal model delta sigma weight residual 92.52 122.56 -30.04 3.00e+00 1.11e-01 1.00e+02 angle pdb=" C42 Q6B A 501 " pdb=" C43 Q6B A 501 " pdb=" C53 Q6B A 501 " ideal model delta sigma weight residual 92.59 121.97 -29.38 3.00e+00 1.11e-01 9.59e+01 angle pdb=" C17 Q6B A 501 " pdb=" C18 Q6B A 501 " pdb=" C33 Q6B A 501 " ideal model delta sigma weight residual 92.63 121.06 -28.43 3.00e+00 1.11e-01 8.98e+01 ... (remaining 4972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 2070 33.90 - 67.81: 65 67.81 - 101.71: 8 101.71 - 135.61: 0 135.61 - 169.52: 4 Dihedral angle restraints: 2147 sinusoidal: 821 harmonic: 1326 Sorted by residual: dihedral pdb=" CA LEU A 345 " pdb=" C LEU A 345 " pdb=" N SER A 346 " pdb=" CA SER A 346 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA GLU A 208 " pdb=" C GLU A 208 " pdb=" N PHE A 209 " pdb=" CA PHE A 209 " ideal model delta harmonic sigma weight residual 180.00 -156.92 -23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" C10 Q6B A 501 " pdb=" C35 Q6B A 501 " pdb=" C36 Q6B A 501 " pdb=" C37 Q6B A 501 " ideal model delta sinusoidal sigma weight residual 56.07 -113.45 169.52 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 2144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 548 0.110 - 0.220: 38 0.220 - 0.330: 5 0.330 - 0.440: 3 0.440 - 0.551: 1 Chirality restraints: 595 Sorted by residual: chirality pdb=" CA GLU A 78 " pdb=" N GLU A 78 " pdb=" C GLU A 78 " pdb=" CB GLU A 78 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.58e+00 chirality pdb=" CA GLU A 406 " pdb=" N GLU A 406 " pdb=" C GLU A 406 " pdb=" CB GLU A 406 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C47 Q6B A 501 " pdb=" C45 Q6B A 501 " pdb=" C49 Q6B A 501 " pdb=" O48 Q6B A 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.90 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 592 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 9 " 0.049 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO B 10 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 82 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 83 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 60 " 0.033 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO A 61 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " 0.028 5.00e-02 4.00e+02 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1033 2.81 - 3.33: 3320 3.33 - 3.85: 5861 3.85 - 4.38: 6348 4.38 - 4.90: 10401 Nonbonded interactions: 26963 Sorted by model distance: nonbonded pdb=" OG1 THR A 419 " pdb=" OD2 ASP B 17 " model vdw 2.284 2.440 nonbonded pdb=" OD1 ASP A 264 " pdb=" OG1 THR A 278 " model vdw 2.297 2.440 nonbonded pdb=" O48 Q6B A 501 " pdb=" O51 Q6B A 501 " model vdw 2.305 2.440 nonbonded pdb=" OG SER A 432 " pdb=" O GLY A 444 " model vdw 2.317 2.440 nonbonded pdb=" OG SER A 58 " pdb=" O THR A 134 " model vdw 2.317 2.440 ... (remaining 26958 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2384 2.51 5 N 581 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.010 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.040 Process input model: 14.390 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:14.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 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 : 0.010 0.163 3679 Z= 0.663 Angle : 1.843 39.884 4977 Z= 0.780 Chirality : 0.072 0.551 595 Planarity : 0.007 0.073 612 Dihedral : 18.570 169.517 1289 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.56 % Favored : 90.21 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.23 % 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: -5.84 (0.26), residues: 429 helix: -3.52 (0.19), residues: 281 sheet: -3.26 (1.21), residues: 10 loop : -4.29 (0.38), residues: 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.391 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 66 average time/residue: 1.0084 time to fit residues: 69.1317 Evaluate side-chains 42 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 40.0000 chunk 11 optimal weight: 40.0000 chunk 23 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 40.0000 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 30.0000 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 397 GLN B 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3679 Z= 0.216 Angle : 1.065 19.236 4977 Z= 0.437 Chirality : 0.040 0.188 595 Planarity : 0.005 0.054 612 Dihedral : 16.208 179.324 495 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 3.74 % 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: -3.99 (0.33), residues: 429 helix: -2.06 (0.26), residues: 279 sheet: -2.66 (1.03), residues: 13 loop : -3.65 (0.42), residues: 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 52 average time/residue: 0.8471 time to fit residues: 46.1870 Evaluate side-chains 49 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.1512 time to fit residues: 1.1400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 40.0000 chunk 11 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 44 optimal weight: 50.0000 chunk 36 optimal weight: 0.3980 chunk 13 optimal weight: 30.0000 chunk 32 optimal weight: 0.0570 chunk 30 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.2904 ------------------------------------------------------------------------------- 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: 0.5896 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3679 Z= 0.180 Angle : 1.000 19.401 4977 Z= 0.401 Chirality : 0.037 0.132 595 Planarity : 0.004 0.050 612 Dihedral : 16.189 177.434 495 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 4.01 % 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: -3.03 (0.37), residues: 429 helix: -1.32 (0.29), residues: 281 sheet: -2.28 (1.22), residues: 13 loop : -3.26 (0.45), residues: 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 42 time to evaluate : 0.431 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 51 average time/residue: 0.8815 time to fit residues: 47.0237 Evaluate side-chains 52 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1423 time to fit residues: 0.7782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3679 Z= 0.187 Angle : 1.027 19.334 4977 Z= 0.411 Chirality : 0.037 0.129 595 Planarity : 0.004 0.047 612 Dihedral : 16.122 178.185 495 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 5.08 % 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: -2.47 (0.39), residues: 429 helix: -0.88 (0.31), residues: 276 sheet: -2.20 (1.26), residues: 13 loop : -3.00 (0.46), residues: 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 63 average time/residue: 0.9276 time to fit residues: 60.8766 Evaluate side-chains 55 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.0225 time to fit residues: 1.6035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 22 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3679 Z= 0.223 Angle : 1.047 19.430 4977 Z= 0.420 Chirality : 0.038 0.161 595 Planarity : 0.005 0.085 612 Dihedral : 16.272 179.098 495 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer Outliers : 4.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.39), residues: 429 helix: -0.68 (0.32), residues: 275 sheet: -3.13 (1.18), residues: 12 loop : -2.83 (0.46), residues: 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 56 average time/residue: 0.9748 time to fit residues: 56.8003 Evaluate side-chains 52 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 2 average time/residue: 0.2175 time to fit residues: 1.1179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 50.0000 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 24 optimal weight: 0.4980 chunk 31 optimal weight: 7.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3679 Z= 0.189 Angle : 1.046 19.355 4977 Z= 0.415 Chirality : 0.038 0.173 595 Planarity : 0.004 0.045 612 Dihedral : 16.110 178.223 495 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer Outliers : 2.94 % 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: -2.07 (0.40), residues: 429 helix: -0.49 (0.32), residues: 273 sheet: -3.06 (1.19), residues: 12 loop : -2.87 (0.47), residues: 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 53 average time/residue: 0.8393 time to fit residues: 46.5965 Evaluate side-chains 52 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 0.1666 time to fit residues: 0.9334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 30.0000 chunk 43 optimal weight: 50.0000 chunk 27 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 0.0010 chunk 8 optimal weight: 30.0000 chunk 29 optimal weight: 7.9990 overall best weight: 4.3994 ------------------------------------------------------------------------------- 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: 0.5852 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3679 Z= 0.202 Angle : 1.043 19.335 4977 Z= 0.416 Chirality : 0.038 0.162 595 Planarity : 0.004 0.046 612 Dihedral : 16.142 178.576 495 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer Outliers : 3.21 % 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: -1.99 (0.40), residues: 429 helix: -0.43 (0.32), residues: 273 sheet: -3.06 (1.15), residues: 12 loop : -2.85 (0.48), residues: 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 54 average time/residue: 0.9068 time to fit residues: 51.1328 Evaluate side-chains 51 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.420 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.5141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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: 0.5888 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3679 Z= 0.216 Angle : 1.084 19.375 4977 Z= 0.431 Chirality : 0.038 0.161 595 Planarity : 0.004 0.043 612 Dihedral : 16.162 179.876 495 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.40), residues: 429 helix: -0.30 (0.32), residues: 272 sheet: -3.09 (1.12), residues: 12 loop : -2.80 (0.48), residues: 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.356 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.9133 time to fit residues: 48.7487 Evaluate side-chains 48 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.1045 time to fit residues: 1.7003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.0000 chunk 42 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.3980 chunk 44 optimal weight: 50.0000 chunk 41 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3679 Z= 0.189 Angle : 1.063 19.379 4977 Z= 0.425 Chirality : 0.038 0.162 595 Planarity : 0.004 0.042 612 Dihedral : 16.036 177.985 495 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.40), residues: 429 helix: -0.15 (0.32), residues: 273 sheet: -3.07 (1.11), residues: 12 loop : -2.76 (0.49), residues: 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.474 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.9113 time to fit residues: 45.8163 Evaluate side-chains 46 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1914 time to fit residues: 0.7769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3679 Z= 0.225 Angle : 1.109 19.377 4977 Z= 0.444 Chirality : 0.039 0.157 595 Planarity : 0.004 0.042 612 Dihedral : 16.109 178.857 495 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer Outliers : 2.14 % 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: -1.72 (0.41), residues: 429 helix: -0.20 (0.32), residues: 273 sheet: -3.11 (1.07), residues: 12 loop : -2.75 (0.50), residues: 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.399 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 0.8408 time to fit residues: 43.1913 Evaluate side-chains 44 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.5475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 50.0000 chunk 6 optimal weight: 30.0000 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 30.0000 chunk 25 optimal weight: 30.0000 chunk 40 optimal weight: 0.0060 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 1 optimal weight: 50.0000 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.160541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.135232 restraints weight = 11824.071| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 3.08 r_work: 0.4266 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.4260 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work: 0.4253 rms_B_bonded: 2.87 restraints_weight: 0.1250 r_work: 0.4246 rms_B_bonded: 2.91 restraints_weight: 0.0625 r_work: 0.4239 rms_B_bonded: 2.97 restraints_weight: 0.0312 r_work: 0.4232 rms_B_bonded: 3.06 restraints_weight: 0.0156 r_work: 0.4224 rms_B_bonded: 3.16 restraints_weight: 0.0078 r_work: 0.4216 rms_B_bonded: 3.28 restraints_weight: 0.0039 r_work: 0.4208 rms_B_bonded: 3.42 restraints_weight: 0.0020 r_work: 0.4199 rms_B_bonded: 3.59 restraints_weight: 0.0010 r_work: 0.4190 rms_B_bonded: 3.78 restraints_weight: 0.0005 r_work: 0.4181 rms_B_bonded: 4.00 restraints_weight: 0.0002 r_work: 0.4171 rms_B_bonded: 4.25 restraints_weight: 0.0001 r_work: 0.4162 rms_B_bonded: 4.54 restraints_weight: 0.0001 r_work: 0.4153 rms_B_bonded: 4.87 restraints_weight: 0.0000 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3679 Z= 0.216 Angle : 1.086 19.383 4977 Z= 0.438 Chirality : 0.038 0.161 595 Planarity : 0.004 0.043 612 Dihedral : 16.029 177.988 495 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.40), residues: 429 helix: -0.22 (0.32), residues: 268 sheet: -3.04 (1.08), residues: 12 loop : -2.62 (0.49), residues: 149 =============================================================================== Job complete usr+sys time: 1538.20 seconds wall clock time: 28 minutes 8.94 seconds (1688.94 seconds total)