Starting phenix.real_space_refine on Sun Mar 10 17:48:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/03_2024/6z3t_11064_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/03_2024/6z3t_11064.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/03_2024/6z3t_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_11064/03_2024/6z3t_11064_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/03_2024/6z3t_11064_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/03_2024/6z3t_11064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/03_2024/6z3t_11064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/03_2024/6z3t_11064_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/03_2024/6z3t_11064_updated.pdb" } resolution = 2.69 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= 0.001 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 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. Process input model Symmetric amino acids flipped Residue "A TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 9": "OE1" <-> "OE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 2.25, per 1000 atoms: 0.62 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: 1.41 Conformation dependent library (CDL) restraints added in 740.7 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: 1.06 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: 0.72 Time building geometry restraints manager: 1.37 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 1.596 1.410 0.186 2.00e-02 2.50e+03 8.61e+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 1.524 1.651 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" CA ASN A 288 " pdb=" C ASN A 288 " ideal model delta sigma weight residual 1.523 1.597 -0.074 1.34e-02 5.57e+03 3.07e+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 85.87 125.77 -39.90 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C12 Q6B A 501 " pdb=" C14 Q6B A 501 " pdb=" C15 Q6B A 501 " ideal model delta sigma weight residual 85.86 125.44 -39.58 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C18 Q6B A 501 " pdb=" C19 Q6B A 501 " pdb=" C20 Q6B A 501 " ideal model delta sigma weight residual 85.88 125.34 -39.46 3.00e+00 1.11e-01 1.73e+02 angle pdb=" C21 Q6B A 501 " pdb=" C22 Q6B A 501 " pdb=" C32 Q6B A 501 " ideal model delta sigma weight residual 92.57 122.56 -29.99 3.00e+00 1.11e-01 9.99e+01 angle pdb=" C42 Q6B A 501 " pdb=" C43 Q6B A 501 " pdb=" C53 Q6B A 501 " ideal model delta sigma weight residual 92.60 121.97 -29.37 3.00e+00 1.11e-01 9.59e+01 ... (remaining 4972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 2079 33.68 - 67.36: 70 67.36 - 101.04: 6 101.04 - 134.72: 4 134.72 - 168.40: 3 Dihedral angle restraints: 2162 sinusoidal: 836 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=" C09 Q6B A 501 " pdb=" C10 Q6B A 501 " pdb=" C35 Q6B A 501 " pdb=" C36 Q6B A 501 " ideal model delta sinusoidal sigma weight residual 281.28 112.88 168.40 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 2159 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=" C10 Q6B A 501 " pdb=" C09 Q6B A 501 " pdb=" C35 Q6B A 501 " pdb=" O11 Q6B A 501 " both_signs ideal model delta sigma weight residual False 2.54 2.92 -0.38 2.00e-01 2.50e+01 3.54e+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 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: 4.050 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: 0.000 Extract box with map and model: 14.370 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 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 0.186 3679 Z= 0.676 Angle : 1.897 39.904 4977 Z= 0.794 Chirality : 0.072 0.551 595 Planarity : 0.007 0.073 612 Dihedral : 19.158 168.398 1304 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 % Allowed : 12.03 % Favored : 86.36 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 193 HIS 0.007 0.002 HIS A 360 PHE 0.018 0.002 PHE A 261 TYR 0.015 0.002 TYR A 457 ARG 0.005 0.001 ARG B 20 *********************** 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 : 0.428 Fit side-chains revert: symmetry clash REVERT: A 271 ARG cc_start: 0.3231 (mmm160) cc_final: -0.0294 (mmm160) REVERT: A 307 MET cc_start: 0.5520 (mmp) cc_final: 0.4589 (mtt) outliers start: 6 outliers final: 1 residues processed: 66 average time/residue: 0.9920 time to fit residues: 67.9614 Evaluate side-chains 43 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE 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: 20.0000 chunk 11 optimal weight: 40.0000 chunk 23 optimal weight: 0.0370 chunk 35 optimal weight: 8.9990 chunk 13 optimal weight: 40.0000 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 30.0000 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 overall best weight: 3.5464 ------------------------------------------------------------------------------- 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: 0.5904 moved from start: 0.2227 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= 0.185 Angle : 1.029 19.228 4977 Z= 0.421 Chirality : 0.039 0.208 595 Planarity : 0.005 0.053 612 Dihedral : 18.133 173.773 512 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.74 % Allowed : 20.59 % Favored : 75.67 % 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: -3.92 (0.34), residues: 429 helix: -2.02 (0.27), residues: 279 sheet: -2.45 (1.04), residues: 13 loop : -3.59 (0.43), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.006 0.001 PHE B 14 TYR 0.009 0.001 TYR A 63 ARG 0.004 0.000 ARG A 66 *********************** 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 : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 ARG cc_start: 0.3012 (mmm160) cc_final: -0.1180 (mmm160) REVERT: A 307 MET cc_start: 0.5641 (mmp) cc_final: 0.4224 (mtt) REVERT: A 449 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7757 (pp) outliers start: 14 outliers final: 5 residues processed: 51 average time/residue: 0.8753 time to fit residues: 46.7069 Evaluate side-chains 49 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 449 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 50.0000 chunk 11 optimal weight: 0.3980 chunk 40 optimal weight: 0.0030 chunk 44 optimal weight: 50.0000 chunk 36 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 0.0370 chunk 30 optimal weight: 8.9990 chunk 21 optimal weight: 0.0270 overall best weight: 1.4928 ------------------------------------------------------------------------------- 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: 0.5850 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3679 Z= 0.150 Angle : 0.983 19.267 4977 Z= 0.390 Chirality : 0.037 0.134 595 Planarity : 0.004 0.049 612 Dihedral : 18.143 177.738 512 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.01 % Allowed : 24.60 % Favored : 71.39 % 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: -3.00 (0.37), residues: 429 helix: -1.33 (0.29), residues: 281 sheet: -2.63 (1.29), residues: 10 loop : -3.14 (0.44), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.001 0.000 HIS A 360 PHE 0.013 0.001 PHE B 53 TYR 0.008 0.001 TYR A 285 ARG 0.002 0.000 ARG A 311 *********************** 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 58 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 271 ARG cc_start: 0.2854 (mmm160) cc_final: -0.0557 (mmm160) REVERT: A 307 MET cc_start: 0.5231 (mmp) cc_final: 0.3883 (mtt) REVERT: A 402 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6444 (tpm170) REVERT: A 449 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7697 (pp) outliers start: 15 outliers final: 6 residues processed: 51 average time/residue: 0.8957 time to fit residues: 47.6948 Evaluate side-chains 54 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 449 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 50.0000 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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: 0.5906 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3679 Z= 0.196 Angle : 1.018 19.225 4977 Z= 0.408 Chirality : 0.038 0.148 595 Planarity : 0.004 0.047 612 Dihedral : 18.034 179.876 512 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.28 % Allowed : 25.40 % Favored : 70.32 % 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 (0.38), residues: 429 helix: -0.93 (0.31), residues: 275 sheet: -1.90 (1.22), residues: 13 loop : -2.98 (0.45), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 193 HIS 0.004 0.001 HIS A 360 PHE 0.009 0.001 PHE B 14 TYR 0.009 0.001 TYR A 457 ARG 0.002 0.000 ARG A 402 *********************** 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 61 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 ARG cc_start: 0.2868 (mmm160) cc_final: -0.0398 (mmm160) REVERT: A 307 MET cc_start: 0.5271 (mmp) cc_final: 0.3867 (mtt) REVERT: A 449 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7765 (pp) outliers start: 16 outliers final: 5 residues processed: 55 average time/residue: 0.9342 time to fit residues: 53.5554 Evaluate side-chains 48 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 449 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 22 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 40.0000 chunk 8 optimal weight: 30.0000 chunk 25 optimal weight: 0.3980 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5900 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3679 Z= 0.181 Angle : 1.013 19.239 4977 Z= 0.401 Chirality : 0.038 0.155 595 Planarity : 0.004 0.047 612 Dihedral : 18.002 178.980 510 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 4.01 % Allowed : 27.27 % Favored : 68.72 % 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: -2.29 (0.39), residues: 429 helix: -0.75 (0.31), residues: 274 sheet: -2.39 (1.08), residues: 15 loop : -2.83 (0.47), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.013 0.001 PHE A 112 TYR 0.009 0.001 TYR A 285 ARG 0.003 0.000 ARG B 12 *********************** 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 59 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ARG cc_start: 0.2882 (mmm160) cc_final: -0.0234 (mmm160) REVERT: A 307 MET cc_start: 0.5243 (mmp) cc_final: 0.3853 (mtt) REVERT: A 402 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6792 (tpm170) REVERT: A 449 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7757 (pp) outliers start: 15 outliers final: 5 residues processed: 52 average time/residue: 0.9431 time to fit residues: 51.0893 Evaluate side-chains 52 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 8 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 20.0000 chunk 43 optimal weight: 50.0000 chunk 36 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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: 0.5974 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3679 Z= 0.265 Angle : 1.081 19.190 4977 Z= 0.436 Chirality : 0.040 0.183 595 Planarity : 0.004 0.049 612 Dihedral : 17.911 177.516 510 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.48 % Allowed : 28.34 % Favored : 68.18 % 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: -2.22 (0.39), residues: 429 helix: -0.65 (0.32), residues: 274 sheet: -3.08 (0.90), residues: 15 loop : -2.82 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 34 HIS 0.006 0.001 HIS A 360 PHE 0.011 0.001 PHE B 14 TYR 0.011 0.002 TYR A 457 ARG 0.003 0.000 ARG A 402 *********************** 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 56 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ARG cc_start: 0.3223 (mmm160) cc_final: 0.0026 (mmm160) REVERT: A 307 MET cc_start: 0.5615 (mmp) cc_final: 0.4173 (mtt) REVERT: A 449 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7763 (pp) outliers start: 13 outliers final: 6 residues processed: 50 average time/residue: 0.9546 time to fit residues: 49.7501 Evaluate side-chains 51 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 449 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 30.0000 chunk 36 optimal weight: 10.0000 chunk 43 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 40.0000 chunk 8 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3679 Z= 0.256 Angle : 1.076 19.211 4977 Z= 0.435 Chirality : 0.040 0.172 595 Planarity : 0.004 0.049 612 Dihedral : 17.942 177.165 510 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.74 % Allowed : 28.34 % Favored : 67.91 % 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: -2.18 (0.39), residues: 429 helix: -0.60 (0.32), residues: 274 sheet: -3.23 (0.89), residues: 15 loop : -2.82 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 34 HIS 0.005 0.001 HIS A 360 PHE 0.010 0.001 PHE A 112 TYR 0.011 0.002 TYR A 457 ARG 0.002 0.000 ARG A 402 *********************** 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 56 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 PHE cc_start: 0.6200 (OUTLIER) cc_final: 0.5939 (m-10) REVERT: A 271 ARG cc_start: 0.3220 (mmm160) cc_final: 0.0043 (mmm160) REVERT: A 307 MET cc_start: 0.5608 (mmp) cc_final: 0.4170 (mtt) REVERT: A 402 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6985 (tpm170) REVERT: A 449 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7732 (pp) REVERT: B 52 PHE cc_start: 0.4279 (OUTLIER) cc_final: 0.3686 (t80) outliers start: 14 outliers final: 5 residues processed: 50 average time/residue: 1.0677 time to fit residues: 55.5077 Evaluate side-chains 51 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 52 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 50.0000 chunk 34 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 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 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3679 Z= 0.216 Angle : 1.081 19.230 4977 Z= 0.435 Chirality : 0.039 0.173 595 Planarity : 0.004 0.049 612 Dihedral : 17.976 177.196 510 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.48 % Allowed : 28.61 % Favored : 67.91 % 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: -2.02 (0.40), residues: 429 helix: -0.47 (0.32), residues: 272 sheet: -3.26 (0.87), residues: 15 loop : -2.73 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.004 0.001 HIS A 360 PHE 0.009 0.001 PHE A 112 TYR 0.009 0.001 TYR A 457 ARG 0.010 0.001 ARG A 66 *********************** 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 57 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 271 ARG cc_start: 0.3073 (mmm160) cc_final: -0.0163 (mmm160) REVERT: A 307 MET cc_start: 0.5643 (mmp) cc_final: 0.4449 (ttm) REVERT: A 402 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6975 (tpm170) REVERT: B 52 PHE cc_start: 0.4377 (OUTLIER) cc_final: 0.3780 (t80) outliers start: 13 outliers final: 7 residues processed: 52 average time/residue: 1.0478 time to fit residues: 56.7073 Evaluate side-chains 51 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 52 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 chunk 26 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 50.0000 chunk 41 optimal weight: 40.0000 chunk 35 optimal weight: 9.9990 chunk 3 optimal weight: 0.0670 overall best weight: 0.9720 ------------------------------------------------------------------------------- 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: 0.5864 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3679 Z= 0.173 Angle : 1.062 19.256 4977 Z= 0.423 Chirality : 0.038 0.163 595 Planarity : 0.004 0.047 612 Dihedral : 18.016 176.958 510 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.41 % Allowed : 29.95 % Favored : 67.65 % 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: -1.83 (0.40), residues: 429 helix: -0.29 (0.32), residues: 274 sheet: -3.13 (0.83), residues: 15 loop : -2.78 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.000 0.000 HIS A 404 PHE 0.010 0.001 PHE A 112 TYR 0.013 0.001 TYR A 302 ARG 0.003 0.000 ARG A 66 *********************** 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 53 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.405 Fit side-chains REVERT: A 271 ARG cc_start: 0.2908 (mmm160) cc_final: -0.1757 (mmt180) REVERT: A 307 MET cc_start: 0.5467 (mmp) cc_final: 0.4254 (ttm) REVERT: A 402 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.7009 (tpt170) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 1.0306 time to fit residues: 53.5447 Evaluate side-chains 49 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 8 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 40.0000 chunk 21 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 0.0270 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 14 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 overall best weight: 7.0048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 300 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3679 Z= 0.255 Angle : 1.120 19.207 4977 Z= 0.456 Chirality : 0.039 0.164 595 Planarity : 0.004 0.047 612 Dihedral : 17.862 175.597 510 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.67 % Allowed : 30.48 % Favored : 66.84 % 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: -1.92 (0.40), residues: 429 helix: -0.42 (0.31), residues: 275 sheet: -3.21 (0.87), residues: 15 loop : -2.68 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.005 0.001 HIS A 360 PHE 0.009 0.001 PHE A 112 TYR 0.010 0.002 TYR A 457 ARG 0.003 0.000 ARG A 66 ********************** 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 53 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.397 Fit side-chains REVERT: A 271 ARG cc_start: 0.3143 (mmm160) cc_final: -0.0096 (mmm160) REVERT: A 307 MET cc_start: 0.5534 (mmp) cc_final: 0.4286 (ttm) REVERT: A 402 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7054 (tpm170) REVERT: A 449 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7769 (pp) REVERT: B 53 PHE cc_start: 0.5775 (OUTLIER) cc_final: 0.5313 (t80) outliers start: 10 outliers final: 5 residues processed: 50 average time/residue: 1.0166 time to fit residues: 52.9161 Evaluate side-chains 48 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 53 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 31 optimal weight: 0.0980 chunk 2 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 0.0570 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 1 optimal weight: 50.0000 chunk 28 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 overall best weight: 3.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.156932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.132896 restraints weight = 12216.077| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 3.09 r_work: 0.4154 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3679 Z= 0.197 Angle : 1.082 19.248 4977 Z= 0.436 Chirality : 0.039 0.161 595 Planarity : 0.004 0.045 612 Dihedral : 17.930 175.585 510 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.41 % Allowed : 31.55 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.40), residues: 429 helix: -0.39 (0.31), residues: 274 sheet: -3.21 (0.85), residues: 15 loop : -2.62 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.002 0.000 HIS A 360 PHE 0.009 0.001 PHE A 112 TYR 0.009 0.001 TYR A 302 ARG 0.004 0.000 ARG A 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1758.08 seconds wall clock time: 32 minutes 16.42 seconds (1936.42 seconds total)