Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 21:31:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/10_2023/6z3t_11064_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/10_2023/6z3t_11064.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/10_2023/6z3t_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_11064/10_2023/6z3t_11064_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/10_2023/6z3t_11064_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/10_2023/6z3t_11064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/10_2023/6z3t_11064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/10_2023/6z3t_11064_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3t_11064/10_2023/6z3t_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-1.21rc1-5097/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: 2.50, per 1000 atoms: 0.69 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: 1.52 Conformation dependent library (CDL) restraints added in 654.1 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: 0.72 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: 0.93 Time building geometry restraints manager: 1.64 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 - 30.48: 2051 30.48 - 60.96: 85 60.96 - 91.44: 7 91.44 - 121.92: 2 121.92 - 152.40: 2 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=" C GLU A 78 " pdb=" N GLU A 78 " pdb=" CA GLU A 78 " pdb=" CB GLU A 78 " ideal model delta harmonic sigma weight residual -122.60 -133.90 11.30 0 2.50e+00 1.60e-01 2.04e+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=" 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: 2.620 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: 14.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.090 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.310 ------------------------------------------------------------------------------- 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 : 17.551 152.396 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 % 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 *********************** 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 : 0.380 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 66 average time/residue: 1.0287 time to fit residues: 70.4802 Evaluate side-chains 42 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.463 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4985 ------------------------------------------------------------------------------- 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: 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: 3.9990 chunk 26 optimal weight: 30.0000 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 overall best weight: 4.8066 ------------------------------------------------------------------------------- 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: 0.5908 moved from start: 0.2207 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= 0.205 Angle : 1.035 19.345 4977 Z= 0.427 Chirality : 0.039 0.197 595 Planarity : 0.005 0.053 612 Dihedral : 12.344 131.258 495 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.74 % Allowed : 21.39 % Favored : 74.87 % 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: -3.96 (0.34), residues: 429 helix: -2.03 (0.27), residues: 279 sheet: -2.67 (1.02), residues: 13 loop : -3.63 (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 : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 52 average time/residue: 0.9171 time to fit residues: 49.8438 Evaluate side-chains 49 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.1452 time to fit residues: 1.0368 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 50.0000 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 44 optimal weight: 50.0000 chunk 36 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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: 0.5937 moved from start: 0.2798 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= 0.250 Angle : 1.022 19.130 4977 Z= 0.420 Chirality : 0.039 0.166 595 Planarity : 0.005 0.052 612 Dihedral : 12.418 132.530 495 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % 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: -3.08 (0.37), residues: 429 helix: -1.31 (0.30), residues: 276 sheet: -3.14 (1.27), residues: 10 loop : -3.26 (0.44), residues: 143 *********************** 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 55 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 39 time to evaluate : 0.438 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 50 average time/residue: 0.8509 time to fit residues: 44.5959 Evaluate side-chains 49 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.2021 time to fit residues: 1.0099 ------------------------------------------------------------------------------- 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: 9.9990 chunk 19 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 50.0000 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.5949 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3679 Z= 0.233 Angle : 1.049 19.156 4977 Z= 0.424 Chirality : 0.039 0.147 595 Planarity : 0.004 0.050 612 Dihedral : 12.382 134.136 495 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 5.88 % Allowed : 26.47 % 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: -2.58 (0.39), residues: 429 helix: -0.95 (0.31), residues: 276 sheet: -3.10 (1.28), residues: 10 loop : -3.00 (0.45), residues: 143 *********************** 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 67 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 0.428 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 5 residues processed: 59 average time/residue: 0.9876 time to fit residues: 60.6363 Evaluate side-chains 51 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.1981 time to fit residues: 0.7721 ------------------------------------------------------------------------------- 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: 5.9990 chunk 17 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 22 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 0.0870 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.3489 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= 0.200 Angle : 1.028 19.170 4977 Z= 0.415 Chirality : 0.038 0.180 595 Planarity : 0.004 0.048 612 Dihedral : 12.360 134.990 495 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.81 % Allowed : 27.54 % 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: -2.29 (0.39), residues: 429 helix: -0.70 (0.31), residues: 276 sheet: -3.56 (1.06), residues: 12 loop : -2.88 (0.47), residues: 141 *********************** 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 68 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 0.419 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 60 average time/residue: 1.1881 time to fit residues: 73.6604 Evaluate side-chains 54 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1731 time to fit residues: 0.9494 ------------------------------------------------------------------------------- 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: 9.9990 chunk 43 optimal weight: 50.0000 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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: 0.5889 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3679 Z= 0.234 Angle : 1.066 19.147 4977 Z= 0.432 Chirality : 0.040 0.186 595 Planarity : 0.004 0.048 612 Dihedral : 12.384 134.850 495 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.74 % Allowed : 30.75 % Favored : 65.51 % 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: -0.59 (0.32), residues: 273 sheet: -3.65 (1.05), residues: 12 loop : -2.95 (0.46), 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 62 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.418 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 58 average time/residue: 1.0469 time to fit residues: 63.1702 Evaluate side-chains 54 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.7214 time to fit residues: 2.0607 ------------------------------------------------------------------------------- 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: 20.0000 chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 40.0000 chunk 25 optimal weight: 20.0000 chunk 13 optimal weight: 40.0000 chunk 8 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 overall best weight: 10.9994 ------------------------------------------------------------------------------- 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: 0.5944 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3679 Z= 0.333 Angle : 1.113 19.097 4977 Z= 0.464 Chirality : 0.042 0.200 595 Planarity : 0.005 0.048 612 Dihedral : 12.538 134.208 495 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.74 % Allowed : 30.48 % Favored : 65.78 % 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: -2.43 (0.39), residues: 429 helix: -0.72 (0.31), residues: 276 sheet: -3.81 (1.07), residues: 12 loop : -3.11 (0.47), residues: 141 *********************** 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 : 0.415 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 52 average time/residue: 0.9751 time to fit residues: 52.8618 Evaluate side-chains 45 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1970 time to fit residues: 0.7749 ------------------------------------------------------------------------------- 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: 9.9990 chunk 4 optimal weight: 50.0000 chunk 34 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.5892 moved from start: 0.4289 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= 0.229 Angle : 1.095 19.185 4977 Z= 0.444 Chirality : 0.039 0.173 595 Planarity : 0.004 0.048 612 Dihedral : 12.421 136.186 495 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.21 % Allowed : 32.35 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.39), residues: 429 helix: -0.63 (0.31), residues: 275 sheet: -3.71 (1.07), residues: 12 loop : -3.15 (0.45), residues: 142 *********************** 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 54 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.426 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 50 average time/residue: 0.9349 time to fit residues: 48.8876 Evaluate side-chains 47 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1838 time to fit residues: 0.7734 ------------------------------------------------------------------------------- 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: 30.0000 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 50.0000 chunk 41 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 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: 0.5852 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3679 Z= 0.201 Angle : 1.071 19.179 4977 Z= 0.433 Chirality : 0.039 0.177 595 Planarity : 0.004 0.047 612 Dihedral : 12.346 137.135 495 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.67 % Allowed : 33.42 % Favored : 63.90 % 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: -0.54 (0.31), residues: 276 sheet: -3.66 (1.03), residues: 12 loop : -3.07 (0.46), residues: 141 *********************** 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 51 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.430 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 0.9237 time to fit residues: 46.4188 Evaluate side-chains 49 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.5811 time to fit residues: 1.7619 ------------------------------------------------------------------------------- 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: 20.0000 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 0.1980 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 40.0000 chunk 9 optimal weight: 50.0000 chunk 35 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 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: 0.5864 moved from start: 0.4626 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= 0.215 Angle : 1.109 19.173 4977 Z= 0.449 Chirality : 0.039 0.163 595 Planarity : 0.007 0.135 612 Dihedral : 12.350 136.647 495 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.67 % Allowed : 33.69 % Favored : 63.64 % 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: -2.01 (0.40), residues: 429 helix: -0.42 (0.32), residues: 275 sheet: -3.65 (1.02), residues: 12 loop : -2.87 (0.48), residues: 142 ********************** 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 49 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.424 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 0.9312 time to fit residues: 46.8397 Evaluate side-chains 45 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1875 time to fit residues: 0.8113 ------------------------------------------------------------------------------- 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: 40.0000 chunk 31 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 1 optimal weight: 50.0000 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.157938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.133087 restraints weight = 12090.420| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 3.12 r_work: 0.4144 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.4677 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= 0.285 Angle : 1.138 19.131 4977 Z= 0.469 Chirality : 0.042 0.173 595 Planarity : 0.007 0.118 612 Dihedral : 12.410 135.238 495 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.60 % Allowed : 34.76 % Favored : 63.64 % 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: -2.15 (0.40), residues: 429 helix: -0.51 (0.32), residues: 275 sheet: -3.77 (1.08), residues: 12 loop : -2.96 (0.47), residues: 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1764.95 seconds wall clock time: 32 minutes 11.19 seconds (1931.19 seconds total)